conda-forge / ambertools-feedstock

A conda-smithy repository for ambertools.

About ambertools-feedstock

Feedstock license: BSD-3-Clause

Home: http://ambermd.org/AmberTools.php

Package license: GPL-3.0-or-later AND LGPL-3.0-or-later AND BSD-3-Clause AND MIT

Summary: AmberTools is a set of programs for biomolecular simulation and analysis

AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the "regular" Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself.

Current build status

Azure

Variant Status linux_64_numpy1.22python3.10.____cpython linux_64_numpy1.22python3.8.____cpython linux_64_numpy1.22python3.9.____cpython linux_64_numpy1.23python3.11.____cpython linux_64_numpy1.26python3.12.____cpython osx_64_numpy1.22python3.10.____cpython osx_64_numpy1.22python3.8.____cpython osx_64_numpy1.22python3.9.____cpython osx_64_numpy1.23python3.11.____cpython osx_64_numpy1.26python3.12.____cpython osx_arm64_numpy1.22python3.10.____cpython osx_arm64_numpy1.22python3.8.____cpython osx_arm64_numpy1.22python3.9.____cpython osx_arm64_numpy1.23python3.11.____cpython osx_arm64_numpy1.26python3.12.____cpython

Current release info

Name	Downloads	Version	Platforms

Installing ambertools

Installing ambertools from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, ambertools can be installed with conda:

conda install ambertools

or with mamba:

mamba install ambertools

It is possible to list all of the versions of ambertools available on your platform with conda:

conda search ambertools --channel conda-forge

or with mamba:

mamba search ambertools --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search ambertools --channel conda-forge

# List packages depending on `ambertools`:
mamba repoquery whoneeds ambertools --channel conda-forge

# List dependencies of `ambertools`:
mamba repoquery depends ambertools --channel conda-forge

About conda-forge

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge Anaconda-Cloud channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating ambertools-feedstock

If you would like to improve the ambertools recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/ambertools-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

• If the version of a package is not being increased, please add or increase the build/number.
• If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

• @dacase
• @j-wags
• @jaimergp
• @mattwthompson
• @mikemhenry
• @simonbray
• @swails

ambertools-feedstock's Issues

re-render package to get current boost-cpp?

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

We've run into issues installing ambertools in the same environment as our analysis package loos. The problems stem from incompatible versions of boost-cpp, which is very finicky about having an exact match in version -- at the conda-forge level, it always pins to a specific very new version. Since ambertools hasn't been re-rendered in a while, we can't make our package build to match yours.

I was wondering if you'd be willing to re-render the ambertools package so that it grabs a current boost-cpp, then we can do the same so the versions match. We're working on a more general solution, but this seems like an easy intermediate step to let our users get back to work.

Thanks,

Alan

PS I'm required to fill in the conda list and conda info fields, but they're irrelevant for this issue.

Installed packages

aoo-mozilla-en-dict-au    2022.08.01           h1a96a4e_0    conda-forge
aoo-mozilla-en-dict-ca    2022.08.01           h1a96a4e_0    conda-forge
aoo-mozilla-en-dict-gb    2022.08.01           h1a96a4e_0    conda-forge
aoo-mozilla-en-dict-us    2022.08.01           hd8ed1ab_0    conda-forge
aoo-mozilla-en-dict-za    2022.08.01           h1a96a4e_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
asttokens                 2.0.8              pyhd8ed1ab_0    conda-forge
atk-1.0                   2.36.0               he69c4ee_4    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
boost                     1.80.0          py311h349b758_2    conda-forge
boost-cpp                 1.80.0               h97e07a4_0    conda-forge
brotli                    1.0.9                hb7f2c08_8    conda-forge
brotli-bin                1.0.9                hb7f2c08_8    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
c-compiler                1.5.1                hbf74d83_0    conda-forge
ca-certificates           2022.12.7            h033912b_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0            h904041c_1014    conda-forge
cctools                   973.0.1             h76f1dac_10    conda-forge
cctools_osx-64            973.0.1             h2b95895_10    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
clang                     14.0.4               h694c41f_0    conda-forge
clang-14                  14.0.4          default_h55ffa42_0    conda-forge
clang_osx-64              14.0.4               h3a95cd4_2    conda-forge
clangxx                   14.0.4          default_h55ffa42_0    conda-forge
clangxx_osx-64            14.0.4               he1dbc44_2    conda-forge
cmake                     3.24.2               h5291bba_0    conda-forge
compiler-rt               14.0.4               h7fcd477_0    conda-forge
compiler-rt_osx-64        14.0.4               h6df654d_0    conda-forge
compilers                 1.5.1                h694c41f_0    conda-forge
contourpy                 1.0.6           py311hd2070f0_0    conda-forge
curl                      7.86.0               h581aaea_0    conda-forge
cxx-compiler              1.5.1                hb8565cd_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
debugpy                   1.6.3           py311h814d153_1    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
doxygen                   1.9.5                h6ca31d6_0    conda-forge
eigen                     3.4.0                h940c156_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.1.1              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hf0c8a7f_0    conda-forge
flake8                    5.0.4              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.1               h5bb23bf_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.38.0          py311h5547dcb_1    conda-forge
fortran-compiler          1.5.1                haad3a49_0    conda-forge
freetype                  2.12.1               h3f81eb7_0    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
gdk-pixbuf                2.42.8               h3648f77_1    conda-forge
gettext                   0.21.1               h8a4c099_0    conda-forge
gfortran                  11.3.0               h2c809b3_0    conda-forge
gfortran_impl_osx-64      11.3.0              h4c39eb8_25    conda-forge
gfortran_osx-64           11.3.0               h18f7dce_0    conda-forge
giflib                    5.2.1                hbcb3906_2    conda-forge
git                       2.38.1          pl5321he9137ab_0    conda-forge
gmp                       6.2.1                h2e338ed_0    conda-forge
graphite2                 1.3.13            h2e338ed_1001    conda-forge
graphviz                  6.0.1                ha8464fc_0    conda-forge
gtk2                      2.24.33              h7c1209e_2    conda-forge
gts                       0.7.6                hccb3bdf_2    conda-forge
h5py                      3.7.0           nompi_py311h777de7a_102    conda-forge
harfbuzz                  5.3.0                h08f8713_0    conda-forge
hdf4                      4.2.15               h0623a88_4    conda-forge
hdf5                      1.12.2          nompi_h1f71328_100    conda-forge
hunspell                  1.7.0             h2df5d5c_1001    conda-forge
hunspell-en               2022.08.01           h1a96a4e_0    conda-forge
icu                       70.1                 h96cf925_0    conda-forge
importlib-metadata        5.0.0              pyha770c72_1    conda-forge
ipykernel                 6.16.2             pyh736e0ef_0    conda-forge
ipython                   8.5.0              pyhd1c38e8_1    conda-forge
isl                       0.22.1               hb1e8313_2    conda-forge
jedi                      0.18.1             pyhd8ed1ab_2    conda-forge
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   hac89ed1_2    conda-forge
jupyter_client            7.4.4              pyhd8ed1ab_0    conda-forge
jupyter_core              4.11.1          py311h6eed73b_1    conda-forge
kiwisolver                1.4.4           py311hd2070f0_1    conda-forge
krb5                      1.19.3               hb98e516_0    conda-forge
lapack                    3.9.0                    netlib    conda-forge
lcms2                     2.14                 h90f4b2a_0    conda-forge
ld64                      609                 hc6ad406_10    conda-forge
ld64_osx-64               609                 h1e06c2b_10    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libblas                   3.9.0           16_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_8    conda-forge
libbrotlidec              1.0.9                hb7f2c08_8    conda-forge
libbrotlienc              1.0.9                hb7f2c08_8    conda-forge
libcblas                  3.9.0           16_osx64_openblas    conda-forge
libclang-cpp14            14.0.4          default_h55ffa42_0    conda-forge
libcurl                   7.86.0               h581aaea_0    conda-forge
libcxx                    14.0.6               hccf4f1f_0    conda-forge
libdeflate                1.14                 hb7f2c08_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgd                     2.3.3                h1e214de_3    conda-forge
libgfortran               5.0.0           10_4_0_h97931a8_25    conda-forge
libgfortran-devel_osx-64  11.3.0              h824d247_25    conda-forge
libgfortran5              11.3.0              h082f757_25    conda-forge
libglib                   2.74.1               h3ba3332_0    conda-forge
libiconv                  1.17                 hac89ed1_0    conda-forge
liblapack                 3.9.0           16_osx64_openblas    conda-forge
libllvm14                 14.0.4               h41df66c_0    conda-forge
libnetcdf                 4.8.1           nompi_hebd45d5_104    conda-forge
libnghttp2                1.47.0               h5aae05b_1    conda-forge
libopenblas               0.3.21          openmp_h429af6e_3    conda-forge
libpng                    1.6.38               ha978bb4_0    conda-forge
librsvg                   2.54.4               h3d48ba6_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.39.4               ha978bb4_0    conda-forge
libssh2                   1.10.0               h47af595_3    conda-forge
libtiff                   4.4.0                hdb44e8a_4    conda-forge
libtool                   2.4.6             he49afe7_1008    conda-forge
libuv                     1.44.2               hac89ed1_0    conda-forge
libwebp                   1.2.4                hfa4350a_0    conda-forge
libwebp-base              1.2.4                h775f41a_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libxml2                   2.10.3               hb9e07b5_0    conda-forge
libzip                    1.9.2                h6db710c_1    conda-forge
libzlib                   1.2.13               hfd90126_4    conda-forge
llvm-openmp               14.0.4               ha654fa7_0    conda-forge
llvm-tools                14.0.4               h41df66c_0    conda-forge
loos                      4.0.4                    pypi_0    pypi
matplotlib                3.6.2           py311h6eed73b_0    conda-forge
matplotlib-base           3.6.2           py311h2bf763f_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mccabe                    0.7.0              pyhd8ed1ab_0    conda-forge
mpc                       1.2.1                hbb51d92_0    conda-forge
mpfr                      4.1.0                h0f52abe_1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
ninja                     1.11.0               h1b54a9f_0    conda-forge
numpy                     1.23.4          py311h62c7003_1    conda-forge
openblas                  0.3.21          openmp_hbefa662_3    conda-forge
openjpeg                  2.5.0                h5d0d7b0_1    conda-forge
openssl                   3.0.7                hfd90126_1    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pango                     1.50.11              h7fca291_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.37                h3f55489_1    conda-forge
perl                      5.32.1          2_h0d85af4_perl5    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.2.0           py311he7df5c9_3    conda-forge
pip                       22.3               pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
prompt-toolkit            3.0.31             pyha770c72_0    conda-forge
psutil                    5.9.3           py311h5547dcb_1    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycodestyle               2.9.1              pyhd8ed1ab_0    conda-forge
pyflakes                  2.5.0              pyhd8ed1ab_0    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
python                    3.11.0          h559f36b_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.11                    2_cp311    conda-forge
pyzmq                     24.0.1          py311habfacb3_1    conda-forge
readline                  8.1.2                h3899abd_0    conda-forge
rhash                     1.4.3                hac89ed1_0    conda-forge
scikit-learn              1.1.3           py311h087fafe_1    conda-forge
scipy                     1.9.3           py311h939689b_1    conda-forge
setuptools                65.5.0             pyhd8ed1ab_0    conda-forge
sigtool                   0.1.3                h88f4db0_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
stack_data                0.5.1              pyhd8ed1ab_0    conda-forge
swig                      4.1.0                haad75c5_3    conda-forge
tapi                      1100.0.11            h9ce4665_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
tornado                   6.2             py311h5547dcb_1    conda-forge
traitlets                 5.5.0              pyhd8ed1ab_0    conda-forge
tzdata                    2022e                h191b570_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.10.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hfd90126_4    conda-forge
zstd                      1.5.2                hfa58983_4    conda-forge

Environment info

active environment : loos
    active env location : /Users/agrossfield/miniconda3/envs/loos
            shell level : 1
       user config file : /Users/agrossfield/.condarc
 populated config files : /Users/agrossfield/.condarc
          conda version : 22.9.0
    conda-build version : not installed
         python version : 3.9.13.final.0
       virtual packages : __osx=12.6=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /Users/agrossfield/miniconda3  (writable)
      conda av data dir : /Users/agrossfield/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/agrossfield/miniconda3/pkgs
                          /Users/agrossfield/.conda/pkgs
       envs directories : /Users/agrossfield/miniconda3/envs
                          /Users/agrossfield/.conda/envs
               platform : osx-64
             user-agent : conda/22.9.0 requests/2.28.1 CPython/3.9.13 Darwin/21.6.0 OSX/12.6
                UID:GID : 1326343926:617926151
             netrc file : None
           offline mode : False

Build on M1 / osx-arm64

Upstreams done! Bot PR here: #80

1. parmed: conda-forge/parmed-feedstock#22
2. netcdf-fortran: conda-forge/netcdf-fortran-feedstock#67
3. packmol: conda-forge/packmol-feedstock#9 conda-forge/packmol-feedstock#12

@conda-forge-admin add python 2.7

Building py27 configurations for a different, derived project. This will not be merged.

OSX builds are bundling some libraries

Trying to update perses so it depends on ambertools instead of Omnia's ambermini results in an error due to clobbing:

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/osx-64::libiconv-1.15-h01d97ff_1005, conda-forge/osx-64::ambertools-19.11-py37h8d9041b_1
  path: 'lib/libiconv.2.dylib'

The environment file used to trigger this behavior is listed here:

Environment

name: perses
channels:
  - conda-forge
  - openeye
  - omnia
  - defaults
​
dependencies:
  - pip
  - python
  - setuptools
  - numpy >=1.14
  - scipy
  - pymbar
  - openmm
  - openmoltools >=0.8.4
  - openmmtools
  - numba
  - netcdf4
  - matplotlib
  - seaborn
  - mdtraj
  - pdbfixer
  - lxml
  - networkx >=2.0
  - openeye-toolkits
  - dask
  - distributed
  - yank
  - progressbar2
  - tqdm

The CMake build system has a step after build where it bundles some libraries in $PREFIX for some reason (see these lines). This might be pulling too many files that are foreign to ambertools. This will need further investigation, I guess, since this step is not needed in Linux.

parmed.version erroneously reports (0,0,0,0)

Issue:
After installing ambertools=20 from conda-forge, parmed.version erroneously reports the incorrect version (0,0,0,0):

$ conda install --yes ambertools=20
>>> import parmed
>>> parmed.version
version(major=0, minor=0, patchlevel=0, commits_ahead=0)

Environment (conda list):

$ conda list
# packages in environment at /Users/choderaj/miniconda/envs/perses:
#
# Name                    Version                   Build  Channel
alabaster                 0.7.12                     py_0    conda-forge
amberlite                 16.0                     pypi_0    pypi
ambertools                17.0                     pypi_0    pypi
appnope                   0.1.0           py37hc8dfbb8_1001    conda-forge
arpack                    3.7.0                hbb27dc6_1    conda-forge
attrs                     18.2.0                   pypi_0    pypi
babel                     2.8.0                      py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
beautifulsoup4            4.8.2            py37hc8dfbb8_1    conda-forge
bleach                    3.1.4              pyh9f0ad1d_0    conda-forge
blosc                     1.17.1               h4a8c4bd_0    conda-forge
bokeh                     2.0.0            py37hc8dfbb8_0    conda-forge
boost                     1.72.0           py37hbf1eeb5_0    conda-forge
boost-cpp                 1.72.0               hdf9ef73_0    conda-forge
bson                      0.5.9                      py_0    conda-forge
bzip2                     1.0.8                h0b31af3_2    conda-forge
ca-certificates           2020.4.5.1           hecc5488_0    conda-forge
cairo                     1.16.0            hec6a9b0_1003    conda-forge
cerberus                  1.3.2                      py_0    conda-forge
certifi                   2020.4.5.1       py37hc8dfbb8_0    conda-forge
cffi                      1.14.0           py37h356ff06_0    conda-forge
cftime                    1.1.1.2          py37h10e2902_0    conda-forge
chardet                   3.0.4           py37hc8dfbb8_1006    conda-forge
click                     6.7                      pypi_0    pypi
cloudpickle               1.3.0                      py_0    conda-forge
clusterutils              0.3.1                    py37_1    omnia
codecov                   2.0.15                     py_1    conda-forge
conda                     4.8.2                    py37_0    conda-forge
conda-build               3.18.12                  py37_1    conda-forge
conda-package-handling    1.6.0            py37h9bfed18_2    conda-forge
contexttimer              0.3.3                    pypi_0    pypi
coverage                  5.0.4            py37h9bfed18_0    conda-forge
cryptography              2.8              py37he655712_2    conda-forge
curl                      7.68.0               h8754def_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
cython                    0.29.16          py37h570ac47_0    conda-forge
cytoolz                   0.10.1           py37h0b31af3_0    conda-forge
dask                      2.10.1                     py_0    conda-forge
dask-core                 2.10.1                     py_0    conda-forge
dbus                      1.13.6               h2f22bb5_0    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
distributed               2.10.0                     py_0    conda-forge
docopt                    0.6.2                      py_1    conda-forge
docutils                  0.16             py37hc8dfbb8_1    conda-forge
entrypoints               0.3             py37hc8dfbb8_1001    conda-forge
expat                     2.2.9                h4a8c4bd_2    conda-forge
ffmpeg                    4.2                  h5c2b479_0    conda-forge
fftw                      3.3.8           nompi_h44ae4c8_1110    conda-forge
fftw3f                    3.3.4                         2    omnia
filelock                  3.0.10                     py_0    conda-forge
fontconfig                2.13.1            h6b1039f_1001    conda-forge
freetype                  2.10.1               h8da9a1a_0    conda-forge
fsspec                    0.7.0                      py_0    conda-forge
gettext                   0.19.8.1          h46ab8bc_1002    conda-forge
glib                      2.58.3          py37h7c187be_1003    conda-forge
glob2                     0.7                        py_0    conda-forge
gmp                       6.2.0                h4a8c4bd_2    conda-forge
gnutls                    3.6.5             h53004b3_1002    conda-forge
hdf4                      4.2.13            h84186c3_1003    conda-forge
hdf5                      1.10.5          nompi_h3e39495_1104    conda-forge
heapdict                  1.0.1                      py_0    conda-forge
icu                       64.2                 h6de7cb9_1    conda-forge
idna                      2.9                        py_1    conda-forge
imagesize                 1.2.0                      py_0    conda-forge
importlib-metadata        1.5.2            py37hc8dfbb8_0    conda-forge
importlib_metadata        1.5.2                         0    conda-forge
ipykernel                 5.2.0            py37h43977f1_1    conda-forge
ipython                   7.13.0           py37hc8dfbb8_2    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.5.1                      py_0    conda-forge
jedi                      0.16.0           py37hc8dfbb8_1    conda-forge
jinja2                    2.11.1                     py_0    conda-forge
joblib                    0.14.1                     py_0    conda-forge
jpeg                      9c                h1de35cc_1001    conda-forge
jsonschema                3.2.0            py37hc8dfbb8_1    conda-forge
jupyter                   1.0.0                      py_2    conda-forge
jupyter_client            6.1.2                      py_0    conda-forge
jupyter_console           6.1.0                      py_1    conda-forge
jupyter_core              4.6.3            py37hc8dfbb8_1    conda-forge
kiwisolver                1.1.0            py37ha1cc60f_1    conda-forge
krb5                      1.16.4               h1752a42_0    conda-forge
lame                      3.100             h1de35cc_1001    conda-forge
latexcodec                2.0.0                      py_0    conda-forge
libarchive                3.3.3             h8912c15_1007    conda-forge
libblas                   3.8.0               16_openblas    conda-forge
libcblas                  3.8.0               16_openblas    conda-forge
libclang                  9.0.1           default_hf57f61e_0    conda-forge
libcurl                   7.68.0               h709d2b2_0    conda-forge
libcxx                    9.0.1                         1    conda-forge
libedit                   3.1.20170329      hcfe32e1_1001    conda-forge
libffi                    3.2.1             h4a8c4bd_1007    conda-forge
libgfortran               4.0.0                         2    conda-forge
libiconv                  1.15              h0b31af3_1006    conda-forge
libidn2                   2.3.0                h0b31af3_0    conda-forge
liblapack                 3.8.0               16_openblas    conda-forge
liblief                   0.9.0                h3e78482_1    conda-forge
libllvm8                  8.0.1                h770b8ee_0    conda-forge
libllvm9                  9.0.1                ha1b3eb9_0    conda-forge
libnetcdf                 4.7.4           nompi_he461dc0_101    conda-forge
libopenblas               0.3.9                h3d69b6c_0    conda-forge
libpng                    1.6.37               hbbe82c9_1    conda-forge
libpq                     12.2                 h554dc5a_0    conda-forge
libsodium                 1.0.17               h01d97ff_0    conda-forge
libssh2                   1.8.2                hcdc9a53_2    conda-forge
libtiff                   4.1.0                h2ae36a8_6    conda-forge
libunistring              0.9.10               h1de35cc_0    conda-forge
libwebp-base              1.1.0                h0b31af3_3    conda-forge
libxcb                    1.13              h1de35cc_1002    conda-forge
libxml2                   2.9.10               h53d96d6_0    conda-forge
libxslt                   1.1.33               h320ff13_0    conda-forge
llvm-openmp               10.0.0               h28b9765_0    conda-forge
llvmlite                  0.31.0           py37hb548287_1    conda-forge
locket                    0.2.0                      py_2    conda-forge
lxml                      4.5.0            py37he54a443_0    conda-forge
lz4-c                     1.8.3             h6de7cb9_1001    conda-forge
lzo                       2.10              h1de35cc_1000    conda-forge
markupsafe                1.1.1            py37h9bfed18_1    conda-forge
matplotlib                3.1.3                    py37_0    conda-forge
matplotlib-base           3.1.3            py37h11da6c2_0    conda-forge
mdtraj                    1.9.3            py37h3e38534_1    conda-forge
mistune                   0.8.4           py37h0b31af3_1000    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
mock                      3.0.5            py37hc8dfbb8_1    conda-forge
more-itertools            8.2.0                      py_0    conda-forge
mpi                       1.0                       mpich    conda-forge
mpich                     3.3.2                hc856adb_0    conda-forge
mpiplus                   v0.0.1                py37_1000    conda-forge
msgpack-python            0.6.2            py37ha1b3eb9_0    conda-forge
nbconvert                 5.6.1                    py37_0    conda-forge
nbformat                  5.0.4                      py_0    conda-forge
ncurses                   6.1               h0a44026_1002    conda-forge
netcdf-fortran            4.5.2           nompi_h0361502_104    conda-forge
netcdf4                   1.5.3           nompi_py37h19ea5d6_103    conda-forge
nettle                    3.4.1             h3efe00b_1002    conda-forge
networkx                  2.4                        py_0    conda-forge
nose                      1.3.7                 py37_1003    conda-forge
nose-timer                0.7.4                      py_0    conda-forge
notebook                  6.0.3                    py37_0    conda-forge
nspr                      4.20              h0a44026_1000    conda-forge
nss                       3.47                 hc0980d9_0    conda-forge
numba                     0.48.0           py37h4f17bb1_0    conda-forge
numexpr                   2.7.1            py37h94625e5_1    conda-forge
numpy                     1.18.1           py37hde6bac1_0    conda-forge
numpydoc                  0.9.2                      py_0    conda-forge
olefile                   0.46                       py_0    conda-forge
openeye-datarecord        0.13.0                   pypi_0    pypi
openeye-drconvert         0.7.0                    pypi_0    pypi
openeye-floe              0.8.11                   pypi_0    pypi
openeye-orionclient       2.6.1                    pypi_0    pypi
openeye-toolkits          2019.10.2                pypi_0    pypi
openforcefield            0.6.0                    py37_1    omnia
openforcefields           1.1.0                    py37_0    omnia
openh264                  1.8.0             hd9629dc_1000    conda-forge
openmm                    7.4.1           py37_cuda101_rc_1    omnia
openmmforcefields         0.7.1+9.gbd2f809.dirty          pypi_0    pypi
openmmtools               0.19.0+25.g2a8537b          pypi_0    pypi
openmoltools              0.0.0.dev0               pypi_0    pypi
openssl                   1.1.1g               h0b31af3_0    conda-forge
oset                      0.1.3                      py_1    conda-forge
packaging                 20.1                       py_0    conda-forge
packmol-memgen            1.1.0rc0                 pypi_0    pypi
pandas                    1.0.3            py37h94625e5_0    conda-forge
pandoc                    2.9.2                         0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parmed                    at20RC5+54.g5702a232fe.dirty          pypi_0    pypi
parso                     0.6.2                      py_0    conda-forge
partd                     1.1.0                      py_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.44                 h4a8c4bd_0    conda-forge
pdb4amber                 1.7.dev0                 pypi_0    pypi
pdbfixer                  1.6                      py37_0    omnia
perl                      5.26.2            haec8ef5_1006    conda-forge
perses                    0.5.1                    pypi_0    pypi
pexpect                   4.8.0            py37hc8dfbb8_1    conda-forge
pickleshare               0.7.5           py37hc8dfbb8_1001    conda-forge
pillow                    7.0.0            py37hfd78ece_1    conda-forge
pip                       20.0.2                   py37_1    conda-forge
pixman                    0.38.0            h01d97ff_1003    conda-forge
pkginfo                   1.5.0.1                    py_0    conda-forge
pluggy                    0.13.0                   py37_0    conda-forge
powerline-status          2.7             py37h0b31af3_1000    conda-forge
progressbar2              3.47.0                     py_0    conda-forge
prometheus_client         0.7.1                      py_0    conda-forge
prompt-toolkit            3.0.5                      py_0    conda-forge
prompt_toolkit            3.0.5                         0    conda-forge
psutil                    5.7.0            py37h9bfed18_1    conda-forge
pthread-stubs             0.4               h1de35cc_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
py                        1.8.1                      py_0    conda-forge
py-lief                   0.9.0            py37h0ceac7d_1    conda-forge
pybtex                    0.22.2           py37hc8dfbb8_1    conda-forge
pybtex-docutils           0.2.2            py37hc8dfbb8_1    conda-forge
pycairo                   1.19.1           py37h4e38901_3    conda-forge
pycosat                   0.6.3           py37h9bfed18_1004    conda-forge
pycparser                 2.20                       py_0    conda-forge
pygments                  2.6.1                      py_0    conda-forge
pymbar                    3.0.5            py37h3b54f70_0    conda-forge
pyopenssl                 19.1.0                     py_1    conda-forge
pyparsing                 2.4.6                      py_0    conda-forge
pyqt                      5.12.3           py37he22c54c_1    conda-forge
pyqt5-sip                 4.19.18                  pypi_0    pypi
pyqtwebengine             5.12.1                   pypi_0    pypi
pyrsistent                0.16.0           py37h9bfed18_0    conda-forge
pysocks                   1.7.1            py37hc8dfbb8_1    conda-forge
pytables                  3.6.1            py37h6f8395a_1    conda-forge
pytest                    5.4.1            py37hc8dfbb8_0    conda-forge
pytest-cov                2.8.1                      py_0    conda-forge
pytest-runner             5.2                        py_0    conda-forge
python                    3.7.6                h5c2c468_2    conda-forge
python-dateutil           2.8.0                    pypi_0    pypi
python-libarchive-c       2.9                      py37_0    conda-forge
python-utils              2.4.0                      py_0    conda-forge
python_abi                3.7                     1_cp37m    conda-forge
pytraj                    2.0.5                    pypi_0    pypi
pytz                      2019.3                     py_0    conda-forge
pyyaml                    5.3.1            py37h9bfed18_0    conda-forge
pyzmq                     19.0.0           py37haec44b1_1    conda-forge
qt                        5.12.5               h514805e_3    conda-forge
qtconsole                 4.7.2              pyh9f0ad1d_0    conda-forge
qtpy                      1.9.0                      py_0    conda-forge
rdkit                     2019.09.3        py37h56de688_1    conda-forge
readline                  8.0                  hcfe32e1_0    conda-forge
requests                  2.23.0             pyh8c360ce_2    conda-forge
requests-toolbelt         0.8.0                    pypi_0    pypi
ripgrep                   11.0.2               h01d97ff_3    conda-forge
ruamel_yaml               0.15.80         py37h9bfed18_1001    conda-forge
sander                    16.0                     pypi_0    pypi
scikit-learn              0.22.2.post1     py37h3dc85bc_0    conda-forge
scipy                     1.4.1            py37h82752d6_0    conda-forge
seaborn                   0.10.0                     py_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                45.1.0                   py37_0    conda-forge
six                       1.14.0                     py_1    conda-forge
smirnoff99frosst          1.1.0                    py37_1    omnia
snowballstemmer           2.0.0                      py_0    conda-forge
sortedcontainers          2.1.0                      py_0    conda-forge
soupsieve                 1.9.4            py37hc8dfbb8_1    conda-forge
sphinx                    2.4.4                      py_0    conda-forge
sphinxcontrib-applehelp   1.0.2                      py_0    conda-forge
sphinxcontrib-bibtex      1.0.0                      py_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    1.0.3                      py_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.4                      py_0    conda-forge
sqlite                    3.30.1               h93121df_0    conda-forge
statsmodels               0.11.1           py37h9bfed18_1    conda-forge
structlog                 18.2.0                   pypi_0    pypi
tabulate                  0.8.7                    pypi_0    pypi
tblib                     1.6.0                      py_0    conda-forge
termcolor                 1.1.0                      py_2    conda-forge
terminado                 0.8.3            py37hc8dfbb8_1    conda-forge
testpath                  0.4.4                      py_0    conda-forge
tinydb                    3.15.2                     py_0    conda-forge
tk                        8.6.10               hbbe82c9_0    conda-forge
toml                      0.10.0                     py_0    conda-forge
toolz                     0.10.0                     py_0    conda-forge
tornado                   6.0.4            py37h9bfed18_1    conda-forge
tqdm                      4.42.1                     py_0    conda-forge
traitlets                 4.3.3            py37hc8dfbb8_1    conda-forge
typing_extensions         3.7.4.1          py37hc8dfbb8_1    conda-forge
urllib3                   1.25.7           py37hc8dfbb8_1    conda-forge
wcwidth                   0.1.9              pyh9f0ad1d_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wget                      1.20.1               h33e2efd_0    conda-forge
wheel                     0.34.2                     py_1    conda-forge
widgetsnbextension        3.5.1                    py37_0    conda-forge
x264                      1!152.20180806       h1de35cc_0    conda-forge
xmltodict                 0.12.0                     py_0    conda-forge
xorg-kbproto              1.0.7             h1de35cc_1002    conda-forge
xorg-libice               1.0.10               h01d97ff_0    conda-forge
xorg-libsm                1.2.3             h01d97ff_1000    conda-forge
xorg-libx11               1.6.9                h0b31af3_0    conda-forge
xorg-libxau               1.0.9                h1de35cc_0    conda-forge
xorg-libxdmcp             1.1.3                h01d97ff_0    conda-forge
xorg-libxext              1.3.4                h01d97ff_0    conda-forge
xorg-libxt                1.2.0                h01d97ff_0    conda-forge
xorg-xextproto            7.3.0             h1de35cc_1002    conda-forge
xorg-xproto               7.0.31            h1de35cc_1007    conda-forge
xz                        5.2.4             h0b31af3_1002    conda-forge
yaml                      0.2.2                h0b31af3_1    conda-forge
yank                      0.25.2                   py37_1    omnia
zeromq                    4.3.2                h6de7cb9_2    conda-forge
zict                      2.0.0                      py_0    conda-forge
zipp                      3.1.0                      py_0    conda-forge
zlib                      1.2.11            h0b31af3_1006    conda-forge
zstd                      1.4.4                hed8d7c8_2    conda-forge

Details about conda and system ( conda info ):

$ conda info

conda info

     active environment : perses
    active env location : /Users/choderaj/miniconda/envs/perses
            shell level : 2
       user config file : /Users/choderaj/.condarc
 populated config files : /Users/choderaj/.condarc
          conda version : 4.8.3
    conda-build version : not installed
         python version : 3.7.6.final.0
       virtual packages : __osx=10.14.6
       base environment : /Users/choderaj/miniconda  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/omnia/osx-64
                          https://conda.anaconda.org/omnia/noarch
                          https://conda.anaconda.org/openeye/osx-64
                          https://conda.anaconda.org/openeye/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/choderaj/miniconda/pkgs
                          /Users/choderaj/.conda/pkgs
       envs directories : /Users/choderaj/miniconda/envs
                          /Users/choderaj/.conda/envs
               platform : osx-64
             user-agent : conda/4.8.3 requests/2.23.0 CPython/3.7.6 Darwin/18.7.0 OSX/10.14.6
                UID:GID : 544813531:9696963
             netrc file : None
           offline mode : False

A release candidate for AmberTools23 is now available

Comment:

@jaimergp The first release candidate for AmberTools23 is now available:

wget https://ambermd.org/downloads/AmberTools23_rc1.tar.bz2

Are you (or someone else connected to this github page) still able and willing to work on this?
You could skip this RC if you wish...a second one should be ready in a week or so. Let me know what I can do to help out.

One change from AmberTools22 is that the NAB compiler is no longer a part of the package. This should be a simplification, and means that users no longer need to the compilers as well as the ambertools package itself.

AmberTools 20 is released

Now that AmberTools 20 has been released, we should update the recipe!

@dacase: Could you put a copy of the AmberTools20.tar.bz2 up at https://ambermd.org/downloads/ like you did for AmberTools19.tar.bz2? We can use the automated update mechanism to keep the package current with patch releases after that!

We'll then be able to update this line, as well as address #27.

CUDA Builds

Comment:

Hi,

I was interested in using some of the CUDA accelerated functionality of cpptraj to speed up some calculations, but it doesn't look like ambertools has any CUDA builds nor is there a separate cpptraj package that I could see similar to how parmed is split out.

Assuming I haven't missed anything (and apologies if I have!), would you be open to providing either a CUDA build of ambertools (assuming that would in turn provide CUDA enabled cpptraj) or alternatively splitting out a separate cpptraj package that itself has a CUDA build available if that is a path of less resistance?

Description of the license for AmberTools needs improvement

Issue: The license for AmberTools is not correctly described.

The README says that the AmberTools license is GPL, but this is too simple. AmberTools is a collection of packages, some GPL, some key ones LGPL, others are BSD, some are public domain. The AmberTools distribution has a LICENSE file (in the AmberTools folder) which explains things carefully.

A key point is that anything that needs to be linked (including all the compiled python modules) are LGPL.

Library issue with ambpdb

Issue:
Not sure if this is the right place for this, but, when I run ambpdb from the conda build of AmberTools I get the following error:

ambpdb: error while loading shared libraries: /home/conda/feedstock_root/build_artifacts/ambertools_1571761492881/work/lib/libcpptraj.so: cannot open shared object file: No such file or directory

Environment (conda list):

Name Version Build Channel

_libgcc_mutex 0.1 main
amberlite 16.0 pypi_0 pypi
ambertools 17.0 pypi_0 pypi
bzip2 1.0.8 h516909a_1 conda-forge
ca-certificates 2019.9.11 hecc5488_0 conda-forge
certifi 2019.9.11 py37_0 conda-forge
cycler 0.10.0 py_2 conda-forge
dbus 1.13.6 he372182_0 conda-forge
expat 2.2.5 he1b5a44_1004 conda-forge
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.0 he983fc9_1 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
glib 2.58.3 h6f030ca_1002 conda-forge
gst-plugins-base 1.14.5 h0935bb2_0 conda-forge
gstreamer 1.14.5 h36ae1b5_0 conda-forge
icu 64.2 he1b5a44_1 conda-forge
jpeg 9c h14c3975_1001 conda-forge
kiwisolver 1.1.0 py37hc9558a2_0 conda-forge
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libclang 9.0.0 hc9558a2_2 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_2 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libllvm9 9.0.0 hc9558a2_3 conda-forge
libopenblas 0.3.7 h6e990d7_3 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libstdcxx-ng 9.1.0 hdf63c60_0
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxkbcommon 0.9.1 hebb1f50_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
matplotlib 3.1.2 py37_0 conda-forge
matplotlib-base 3.1.2 py37h250f245_0 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
ncurses 6.1 hf484d3e_1002 conda-forge
nspr 4.23 he1b5a44_0 conda-forge
nss 3.47 he751ad9_0 conda-forge
numpy 1.17.3 py37h95a1406_0 conda-forge
openssl 1.1.1d h516909a_0 conda-forge
packmol-memgen 1.0.5rc0 pypi_0 pypi
parmed 3.2.0 pypi_0 pypi
pcre 8.43 he1b5a44_0 conda-forge
pdb4amber 1.7.dev0 pypi_0 pypi
pip 19.3.1 py37_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
pyparsing 2.4.4 py_0 conda-forge
pyqt 5.12.3 py37hcca6a23_0 conda-forge
pyqt5-sip 4.19.18 pypi_0 pypi
pyqtwebengine 5.12.1 pypi_0 pypi
python 3.7.3 h33d41f4_1 conda-forge
python-dateutil 2.8.1 py_0 conda-forge
pytraj 2.0.5 pypi_0 pypi
qt 5.12.5 hd8c4c69_1 conda-forge
readline 8.0 hf8c457e_0 conda-forge
sander 16.0 pypi_0 pypi
scipy 1.3.1 py37h921218d_2 conda-forge
setuptools 41.6.0 py37_1 conda-forge
six 1.13.0 py37_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
tk 8.6.9 hed695b0_1003 conda-forge
tornado 6.0.3 py37h516909a_0 conda-forge
wheel 0.33.6 py37_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge

Details about conda and system ( conda info ):

 active environment : test
active env location : /home/dave/anaconda3/envs/test
        shell level : 3
   user config file : /home/dave/.condarc

populated config files :
conda version : 4.7.12
conda-build version : 3.18.9
python version : 3.7.3.final.0
virtual packages : __cuda=10.1
base environment : /home/dave/anaconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/dave/anaconda3/pkgs
/home/dave/.conda/pkgs
envs directories : /home/dave/anaconda3/envs
/home/dave/.conda/envs
platform : linux-64
user-agent : conda/4.7.12 requests/2.21.0 CPython/3.7.3 Linux/4.15.0-66-generic ubuntu/18.04.3 glibc/2.27
UID:GID : 1000:1000
netrc file : None
offline mode : False

Antechamber bug in Ambertools 22 package on Intel macs upgraded to OSX 13

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Debugging a recent issue at OpenFF seems to indicate that Antechamber from AT22 has a fatal problem parsing inputs on intel-based macbooks that upgrade to OSX 13.

This issue does not reproduce on

• ARM-based macs on either OSX 12 or 13
• The same Intel-based mac before it was upgraded from OSX 12 to 13
• The same Intel-based mac using OSX 13 and downgraded to AmberTools 20 or 21

To reproduce:

molecule.tar.gz

antechamber -i molecule.sdf -fi sdf -o sqm.in -fo sqmcrt -pf yes -c mul -nc 0

Unsuccessful outputs on Intel mac upgraded to OSX 13 and using AT22:

Terminal output

Welcome to antechamber 22.0: molecular input file processor.

Info: acdoctor mode is on: check and diagnose problems in the input file.
Info: The atom type is set to gaff; the options available to the -at flag are
      gaff, gaff2, amber, bcc, and sybyl.

-- Check Format for sdf File --
   Status: pass
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
Warning: This molecule has no hydrogens nor halogens.
         It is quite possible that there are unfilled valences.
-- Check Geometry --
      for those bonded   
      for those not bonded   
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Info: Total number of electrons: 0; net charge: 0

Running: /Users/jeffreywagner/miniconda3/envs/offtk-0106/bin/sqm -O -i sqm.in -o sqm.out
/Users/jeffreywagner/miniconda3/envs/offtk-0106/bin/wrapped_progs/antechamber: Fatal Error!
Cannot properly run "/Users/jeffreywagner/miniconda3/envs/offtk-0106/bin/sqm -O -i sqm.in -o sqm.out".

sqm.in contents:

Run semi-empirical minimization
 &qmmm
    qm_theory='AM1', grms_tol=0.0005,
 scfconv=1.d-10, ndiis_attempts=700,   qmcharge=0,
 /

Successful outputs on Intel mac upgraded to OSX 13 and using AT21 (downgraded AT):

Terminal output:

Welcome to antechamber 21.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for sdf File --
   Status: pass
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded   
      for those not bonded   
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Info: Total number of electrons: 80; net charge: 0

Running: /Users/jeffreywagner/miniconda3/envs/offtk-0106-at21/bin/sqm -O -i sqm.in -o sqm.out
Info: Total number of electrons: 80; net charge: 0

sqm.in contents:

Run semi-empirical minimization
 &qmmm
    qm_theory='AM1', grms_tol=0.0005,
 scfconv=1.d-10, ndiis_attempts=700,   qmcharge=0,
 /
   6    C1        3.7930        0.2790        0.1180 
   6    C2        2.3140        0.5510       -0.0250 
   8    O1        2.0090        1.7310       -0.2650 
   7    N1        1.3590       -0.4630        0.1070 
   6    C3       -0.0420       -0.2930       -0.0170 
   6    C4       -0.6350        0.8400       -0.5250 
   6    C5       -2.0270        0.9560       -0.6070 
   6    C6       -2.8590       -0.0390       -0.1920 
   6    C7       -2.2710       -1.1800        0.3200 
   6    C8       -0.9090       -1.3080        0.4060 
   8    O2       -4.2440        0.0160       -0.2470 
   1    H1        4.3410        0.9350       -0.5910 
   1    H2        4.0170       -0.7900       -0.1110 
   1    H3        4.0770        0.4680        1.1820 
   1    H4        1.6870       -1.4560        0.3140 
   1    H5       -0.0620        1.6810       -0.8900 
   1    H6       -2.4700        1.8620       -1.0130 
   1    H7       -2.9200       -1.9910        0.6590 
   1    H8       -0.4290       -2.1970        0.8060 
   1    H9       -4.7260        0.3990        0.5700 

Installed packages

UNSUCCESSFUL env

# packages in environment at /Users/jeffreywagner/miniconda3/envs/offtk-0106:
#
# Name                    Version                   Build  Channel
amberlite                 22.0                     pypi_0    pypi
ambertools                22.0            py310h35066de_3    conda-forge
amberutils                21.0                     pypi_0    pypi
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0                   pypi_0    pypi
arpack                    3.7.0                hefb7bc6_2    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.2             pyha770c72_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.2               hebb52c4_0    conda-forge
boost                     1.74.0          py310h509978a_5    conda-forge
boost-cpp                 1.74.0               h8b082ac_8    conda-forge
brotli                    1.0.9                hb7f2c08_8    conda-forge
brotli-bin                1.0.9                hb7f2c08_8    conda-forge
brotlipy                  0.7.0                    pypi_0    pypi
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
ca-certificates           2022.12.7            h033912b_0    conda-forge
cairo                     1.16.0            h904041c_1014    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1                   pypi_0    pypi
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7                    pypi_0    pypi
cryptography              39.0.1                   pypi_0    pypi
curl                      7.88.1               h6df9250_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.33                  pypi_0    pypi
debugpy                   1.6.6                    pypi_0    pypi
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hf0c8a7f_0    conda-forge
fftw                      3.3.10          nompi_h4fa670e_106    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h5bb23bf_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.38.0                   pypi_0    pypi
freetype                  2.12.1               h3f81eb7_1    conda-forge
gettext                   0.21.1               h8a4c099_0    conda-forge
greenlet                  2.0.2                    pypi_0    pypi
hdf4                      4.2.15               h7aa5921_5    conda-forge
hdf5                      1.12.2          nompi_h48135f9_101    conda-forge
icu                       70.1                 h96cf925_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.0.0              pyha770c72_0    conda-forge
importlib_metadata        6.0.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.21.2             pyh736e0ef_0    conda-forge
ipython                   8.10.0             pyhd1c38e8_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jpeg                      9e                   hb7f2c08_3    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter-core              5.2.0                    pypi_0    pypi
jupyter_client            8.0.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.2.0           py310h2ec42d9_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.3.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
khronos-opencl-icd-loader 2022.09.30           hb7f2c08_2    conda-forge
kiwisolver                1.4.4                    pypi_0    pypi
krb5                      1.20.1               h049b76e_0    conda-forge
lcms2                     2.14                 h29502cd_1    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libaec                    1.0.6                hf0c8a7f_1    conda-forge
libblas                   3.9.0           16_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_8    conda-forge
libbrotlidec              1.0.9                hb7f2c08_8    conda-forge
libbrotlienc              1.0.9                hb7f2c08_8    conda-forge
libcblas                  3.9.0           16_osx64_openblas    conda-forge
libcurl                   7.88.1               h6df9250_0    conda-forge
libcxx                    14.0.6               hccf4f1f_0    conda-forge
libdeflate                1.17                 hac1461d_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           10_4_0_h97931a8_28    conda-forge
libgfortran5              11.3.0              h082f757_28    conda-forge
libglib                   2.74.1               h4c723e1_1    conda-forge
libiconv                  1.17                 hac89ed1_0    conda-forge
liblapack                 3.9.0           16_osx64_openblas    conda-forge
libnetcdf                 4.8.1           nompi_hc61b76e_106    conda-forge
libnghttp2                1.51.0               he2ab024_0    conda-forge
libopenblas               0.3.21          openmp_h429af6e_3    conda-forge
libpng                    1.6.39               ha978bb4_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.40.0               ha978bb4_0    conda-forge
libssh2                   1.10.0               h47af595_3    conda-forge
libtiff                   4.5.0                hee9004a_2    conda-forge
libwebp-base              1.2.4                h775f41a_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libxml2                   2.10.3               hb9e07b5_0    conda-forge
libzip                    1.9.2                h6db710c_1    conda-forge
libzlib                   1.2.13               hfd90126_4    conda-forge
llvm-openmp               15.0.7               h61d9ccf_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
markupsafe                2.1.2                    pypi_0    pypi
matplotlib                3.7.0                    pypi_0    pypi
matplotlib-base           3.7.0           py310he725631_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdtraj                    1.9.7                    pypi_0    pypi
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclassic                 0.5.2              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.2              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.9              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.0           nompi_h96bf37d_102    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
notebook                  6.5.2              pyha770c72_1    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
numexpr                   2.8.3                    pypi_0    pypi
numpy                     1.24.2                   pypi_0    pypi
ocl_icd_wrapper_apple     1.0.0                hbcb3906_0    conda-forge
openff-forcefields        2.0.0              pyh6c4a22f_0    conda-forge
openff-toolkit            0.10.6+0.g37d6806b.dirty           dev_0    <develop>
openjpeg                  2.5.0                h13ac156_2    conda-forge
openmm                    8.0.0                    pypi_0    pypi
openssl                   3.0.8                hfd90126_0    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h508aa58_0    conda-forge
packmol-memgen            1.2.3rc0                 pypi_0    pypi
pandas                    1.5.3                    pypi_0    pypi
pandoc                    2.19.2               h694c41f_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parmed                    3.4.3                    pypi_0    pypi
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                h1c4e4bc_0    conda-forge
pdb4amber                 22.0                     pypi_0    pypi
perl                      5.32.1          2_h0d85af4_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.4.0                    pypi_0    pypi
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.0.0              pyhd8ed1ab_0    conda-forge
pooch                     1.6.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.36             pyha770c72_0    conda-forge
psutil                    5.9.4                    pypi_0    pypi
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycairo                   1.23.0                   pypi_0    pypi
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pymsmt                    22.0                     pypi_0    pypi
pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3                   pypi_0    pypi
pysocks                   1.7.1                    pypi_0    pypi
pytables                  3.7.0           py310h90ba602_3    conda-forge
python                    3.10.9          he7542f4_0_cpython    conda-forge
python-constraint         1.4.0                      py_0    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.6              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
pyyaml                    6.0                      pypi_0    pypi
pyzmq                     25.0.0                   pypi_0    pypi
rdkit                     2022.09.1       py310h5b22e64_0    conda-forge
readline                  8.1.2                h3899abd_0    conda-forge
reportlab                 3.6.12                   pypi_0    pypi
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
sander                    22.0                     pypi_0    pypi
scipy                     1.10.0                   pypi_0    pypi
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                67.3.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge
snappy                    1.1.9                h225ccf5_2    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sqlalchemy                2.0.4                    pypi_0    pypi
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
tables                    3.7.0                    pypi_0    pypi
terminado                 0.17.1             pyhd1c38e8_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
tornado                   6.2                      pypi_0    pypi
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.4.0                hd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022g                h191b570_0    conda-forge
unicodedata2              15.0.0                   pypi_0    pypi
urllib3                   1.26.14            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.1              pyhd8ed1ab_0    conda-forge
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h35c211d_1002    conda-forge
xorg-libice               1.0.10               h0d85af4_0    conda-forge
xorg-libsm                1.2.3             h0d85af4_1000    conda-forge
xorg-libx11               1.7.2                h0d85af4_0    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xorg-libxext              1.3.4                h0d85af4_1    conda-forge
xorg-libxt                1.2.1                h0d85af4_2    conda-forge
xorg-xextproto            7.3.0             h35c211d_1002    conda-forge
xorg-xproto               7.0.31            h35c211d_1007    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.14.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hfd90126_4    conda-forge
zstd                      1.5.2                hbc0c0cd_6    conda-forge

SUCCESSFUL env

# packages in environment at /Users/jeffreywagner/miniconda3/envs/offtk-0106-at21:
#
# Name                    Version                   Build  Channel
ambertools                21.12            py39hf80593e_0    conda-forge
amberutils                21.0                     pypi_0    pypi
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39ha30fb19_3    conda-forge
arpack                    3.7.0                hefb7bc6_2    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.2             pyha770c72_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.2               hebb52c4_0    conda-forge
boost                     1.74.0           py39ha1f3e3e_5    conda-forge
boost-cpp                 1.74.0               h8b082ac_8    conda-forge
brotli                    1.0.9                hb7f2c08_8    conda-forge
brotli-bin                1.0.9                hb7f2c08_8    conda-forge
brotlipy                  0.7.0           py39ha30fb19_1005    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
ca-certificates           2022.12.7            h033912b_0    conda-forge
cairo                     1.16.0            h904041c_1014    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py39h131948b_3    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7            py39h92daf61_0    conda-forge
cryptography              39.0.0           py39h7eb6a14_0    conda-forge
curl                      7.87.0               haf73cf8_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.33          py39h7a8716b_0    conda-forge
debugpy                   1.6.6            py39h7a8716b_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hf0c8a7f_0    conda-forge
fftw                      3.3.10          nompi_h4fa670e_106    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h5bb23bf_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.38.0           py39ha30fb19_1    conda-forge
freetype                  2.12.1               h3f81eb7_1    conda-forge
gettext                   0.21.1               h8a4c099_0    conda-forge
greenlet                  2.0.2            py39h7a8716b_0    conda-forge
hdf4                      4.2.15               h7aa5921_5    conda-forge
hdf5                      1.12.2          nompi_h70e9adf_101    conda-forge
icu                       70.1                 h96cf925_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.0.0              pyha770c72_0    conda-forge
importlib-resources       5.12.0             pyhd8ed1ab_0    conda-forge
importlib_metadata        6.0.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.21.2             pyh736e0ef_0    conda-forge
ipython                   8.10.0             pyhd1c38e8_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jpeg                      9e                   hb7f2c08_3    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            8.0.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.2.0            py39h6e9494a_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.3.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
khronos-opencl-icd-loader 2022.09.30           hb7f2c08_2    conda-forge
kiwisolver                1.4.4            py39h92daf61_1    conda-forge
krb5                      1.20.1               h0165f36_0    conda-forge
lcms2                     2.14                 h29502cd_1    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libaec                    1.0.6                hf0c8a7f_1    conda-forge
libblas                   3.9.0           16_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_8    conda-forge
libbrotlidec              1.0.9                hb7f2c08_8    conda-forge
libbrotlienc              1.0.9                hb7f2c08_8    conda-forge
libcblas                  3.9.0           16_osx64_openblas    conda-forge
libcurl                   7.87.0               haf73cf8_0    conda-forge
libcxx                    14.0.6               hccf4f1f_0    conda-forge
libdeflate                1.17                 hac1461d_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           10_4_0_h97931a8_28    conda-forge
libgfortran5              11.3.0              h082f757_28    conda-forge
libglib                   2.74.1               h4c723e1_1    conda-forge
libiconv                  1.17                 hac89ed1_0    conda-forge
liblapack                 3.9.0           16_osx64_openblas    conda-forge
libnetcdf                 4.8.1           nompi_hc61b76e_106    conda-forge
libnghttp2                1.51.0               h0dd9d14_0    conda-forge
libopenblas               0.3.21          openmp_h429af6e_3    conda-forge
libpng                    1.6.39               ha978bb4_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.40.0               ha978bb4_0    conda-forge
libssh2                   1.10.0               h7535e13_3    conda-forge
libtiff                   4.5.0                hee9004a_2    conda-forge
libwebp-base              1.2.4                h775f41a_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libxml2                   2.10.3               hb9e07b5_0    conda-forge
libzip                    1.9.2                h3ad4413_1    conda-forge
libzlib                   1.2.13               hfd90126_4    conda-forge
llvm-openmp               15.0.7               h61d9ccf_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
markupsafe                2.1.2            py39ha30fb19_0    conda-forge
matplotlib-base           3.7.0            py39hb2f573b_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdtraj                    1.9.7            py39h5456c6e_4    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
mock                      5.0.1              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclassic                 0.5.2              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.2              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.9              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.5.4           nompi_h96bf37d_102    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
notebook                  6.5.2              pyha770c72_1    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
numexpr                   2.8.3            py39hecff1ad_1    conda-forge
numpy                     1.24.2           py39h6ee2318_0    conda-forge
ocl_icd_wrapper_apple     1.0.0                hbcb3906_0    conda-forge
openff-forcefields        2.0.0              pyh6c4a22f_0    conda-forge
openff-toolkit            0.10.6+0.g37d6806b.dirty           dev_0    <develop>
openjpeg                  2.5.0                h13ac156_2    conda-forge
openmm                    8.0.0           py39h54c61d6_0_khronos    conda-forge
openssl                   1.1.1t               hfd90126_0    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h508aa58_0    conda-forge
packmol-memgen            1.2.1rc0                 pypi_0    pypi
pandas                    1.5.3            py39hecff1ad_0    conda-forge
pandoc                    2.19.2               h694c41f_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parmed                    3.4.4            py39h7a8716b_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                h1c4e4bc_0    conda-forge
perl                      5.32.1          2_h0d85af4_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5           py39hde42818_1002    conda-forge
pillow                    9.4.0            py39h7f5cd59_1    conda-forge
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.0.0              pyhd8ed1ab_0    conda-forge
pooch                     1.6.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.36             pyha770c72_0    conda-forge
psutil                    5.9.4            py39ha30fb19_0    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycairo                   1.23.0           py39h41776c8_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3           py39ha30fb19_0    conda-forge
pysocks                   1.7.1            py39h6e9494a_5    conda-forge
pytables                  3.7.0            py39hc15ac9a_3    conda-forge
python                    3.9.15          h531fd05_0_cpython    conda-forge
python-constraint         1.4.0                      py_0    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      3_cp39    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py39ha30fb19_5    conda-forge
pyzmq                     25.0.0           py39hed8f129_0    conda-forge
rdkit                     2022.09.1        py39h67dd817_0    conda-forge
readline                  8.1.2                h3899abd_0    conda-forge
reportlab                 3.6.12           py39h4e200fb_2    conda-forge
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
sander                    16.0                     pypi_0    pypi
scipy                     1.10.0           py39h8a15683_2    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                67.4.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge
snappy                    1.1.9                h225ccf5_2    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sqlalchemy                2.0.4            py39ha30fb19_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyhd1c38e8_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
tornado                   6.2              py39ha30fb19_1    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.4.0                hd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022g                h191b570_0    conda-forge
unicodedata2              15.0.0           py39ha30fb19_0    conda-forge
urllib3                   1.26.14            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.1              pyhd8ed1ab_0    conda-forge
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h35c211d_1002    conda-forge
xorg-libice               1.0.10               h0d85af4_0    conda-forge
xorg-libsm                1.2.3             h0d85af4_1000    conda-forge
xorg-libx11               1.7.2                h0d85af4_0    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xorg-libxext              1.3.4                hb7f2c08_2    conda-forge
xorg-libxt                1.2.1                h0d85af4_2    conda-forge
xorg-xextproto            7.3.0             hb7f2c08_1003    conda-forge
xorg-xproto               7.0.31            h35c211d_1007    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.14.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hfd90126_4    conda-forge
zstd                      1.5.2                hbc0c0cd_6    conda-forge

Environment info

active environment : offtk-0106-at21
    active env location : /Users/jeffreywagner/miniconda3/envs/offtk-0106-at21
            shell level : 1
       user config file : /Users/jeffreywagner/.condarc
 populated config files : /Users/jeffreywagner/.condarc
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.8.3.final.0
       virtual packages : __osx=10.16=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /Users/jeffreywagner/miniconda3  (writable)
      conda av data dir : /Users/jeffreywagner/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/omnia/osx-64
                          https://conda.anaconda.org/omnia/noarch
                          https://conda.anaconda.org/openeye/osx-64
                          https://conda.anaconda.org/openeye/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/jeffreywagner/miniconda3/pkgs
                          /Users/jeffreywagner/.conda/pkgs
       envs directories : /Users/jeffreywagner/miniconda3/envs
                          /Users/jeffreywagner/.conda/envs
               platform : osx-64
             user-agent : conda/4.10.3 requests/2.24.0 CPython/3.8.3 Darwin/22.3.0 OSX/10.16
                UID:GID : 501:20
             netrc file : None
           offline mode : False

We need to work on creating a conda package for AmberTools22, which will be released soon

Comment:

The release of AmberTools22 should be ready later this month (April, 2022). We have release candidates ready, but I'd like to find out what problems (if any) we will find in updating the current conda packages. Here is the updated URL

https://ambermd.org/downloads/AmberTools22.02apr22.tar.bz2

In the ideal world, one could substitute the new URL for the existing one in the meta.yaml file. I don't see any obvious problems in build.sh, but the code changes are pretty big, so something is likely to break....For sure, the three patch files invoked after downloading the source are unlikely to apply cleanly.

Unfortunately, I am not much of a conda or conda-forge person. I edited build.sh to skip the update_amber step, and tried conda build recipe. Pretty early on I encountered a version problem with cpptraj:

+ rm /Users/case/conda-bld/ambertools_1649863164081/work/AmberTools/src/cpptraj/src/xdrfile/version
rm: /Users/case/conda-bld/ambertools_1649863164081/work/AmberTools/src/cpptraj/src/xdrfile/version: No such file or directory

I could try to track this down, but it seems likely that someone (@jaimergp @simonbray ?) would be much more likely to know what to do here, and in whatever pops up next. But let me know how I can help, if needed.

...thanks!....dac

input_parser.py ValueError: invalid literal for int() with base 10: ''

Comment:

Hi,

I am trying to calculate MMPBSA and MMGBSA by using Ambertools and OpenMM in Google colab from this notebook. The code below is what I run:

import os
!conda install -c conda-forge -c openbabel -c bioconda -y openmm openmm-setup openbabel ambertools compilers pdbfixer gromacs

os.environ['AMBERHOME'] = "/usr/local"
!echo $AMBERHOME
!source "$AMBERHOME/amber.sh"
!MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA_decomposition.dat -sp  complex.prmtop -cp com.prmtop -rp rec.prmtop -lp ligand.prmtop -y prot_lig_prod_all.dcd

I create mmpbsa.in by using:

f = open("mmpbsa.in", "w")
f.write("""&general """  + "\n"
"""  endframe=""" + """,  interval=""" + """, strip_mask=:WAT:Na+:Cl-:Mg+:K+, """ + "\n"
"""/ """ + "\n"
"""&gb """ + "\n"
""" igb=""" +  """, saltcon=""" +  """, """ + "\n"
"""/""")
f.close()

The error is:

  File "/usr/local/bin/MMPBSA.py", line 90, in <module>
    app.read_input_file()
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 762, in read_input_file
    self.INPUT = self.input_file.Parse(infile)
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/input_parser.py", line 443, in Parse
    SetValue(var[1])
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/input_parser.py", line 112, in SetValue
    self.value = self.datatype(value)
ValueError: invalid literal for int() with base 10: ''

Fatal Error! 
All files have been retained for your error investigation: 
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.

My files here:
MMGBSA_input.zip

Please help me to fix this error. Thank you very much,

CPU overload

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue:
I'm not sure if this bug is reported here, although it is explicitly related to the conda ambertools package.

I have a project that depends on AmberTools and ever since I discovered the conda package I have used it. However, it wasn't until recently that I realized that the programs I use from AmberTools overload the CPU. I thought it was a specific program, but doing the relevant tests I realized that they are all (at least the ones I use: sander, mmpbsa_py_nmode, rism3d.snglpnt, and I'm not sure if the same thing happens to cpptraj).
The programs, even if they are executed in a single thread serially, end up consuming 1500% of that core, but in practice, it means that it occupies all the available cores. This doesn't happen with the compiled version of AmberTools, so it seems to be an issue with this build. I also tried several versions (21.1-21.12) and in all of them, I get the same result. I even downloaded the package that uses the conda recipe and compiled it on my PC and I get the same problem. I hope you can give me information about it.

Mario S.

Environment (conda list):

# packages in environment at /home/mario/programs/miniconda3.9/envs/conda_at21:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
ambertools                21.12            py39hc630cb1_0    file:///home/mario/Documents/ambertools-feedstock-master/build_artifacts
amberutils                21.0                     pypi_0    pypi
arpack                    3.7.0                hdefa2d7_2    conda-forge
boost-cpp                 1.74.0               h6cacc03_7    conda-forge
brotli                    1.0.9                h7f98852_6    conda-forge
brotli-bin                1.0.9                h7f98852_6    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
certifi                   2021.10.8        py39hf3d152e_1    conda-forge
curl                      7.81.0               h2574ce0_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.28          py39he80948d_0    conda-forge
fftw                      3.3.10          nompi_h77c792f_102    conda-forge
fonttools                 4.29.1           py39h3811e60_0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.12.1          nompi_h2750804_103    conda-forge
icu                       69.1                 h9c3ff4c_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jpeg                      9e                   h7f98852_0    conda-forge
kiwisolver                1.3.2            py39h1a9c180_1    conda-forge
krb5                      1.19.2               hcc1bbae_3    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           13_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h7f98852_6    conda-forge
libbrotlidec              1.0.9                h7f98852_6    conda-forge
libbrotlienc              1.0.9                h7f98852_6    conda-forge
libcblas                  3.9.0           13_linux64_openblas    conda-forge
libcurl                   7.81.0               h2574ce0_0    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 11.2.0              h1d223b6_12    conda-forge
libgfortran-ng            11.2.0              h69a702a_12    conda-forge
libgfortran5              11.2.0              h5c6108e_12    conda-forge
libgomp                   11.2.0              h1d223b6_12    conda-forge
liblapack                 3.9.0           13_linux64_openblas    conda-forge
libnetcdf                 4.8.1           nompi_hb3fd0d9_101    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_12    conda-forge
libtiff                   4.3.0                h542a066_3    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libzip                    1.8.0                h4de3113_1    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
llvm-openmp               13.0.1               hf817b99_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
matplotlib-base           3.5.1            py39h2fa2bec_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.3                  h9c3ff4c_0    conda-forge
netcdf-fortran            4.5.4           nompi_h2b6e579_100    conda-forge
numpy                     1.22.2           py39h91f2184_0    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h86c2bf4_0    conda-forge
packmol-memgen            1.2.1rc0                 pypi_0    pypi
pandas                    1.4.1            py39hde0f152_0    conda-forge
parmed                    3.4.3            py39he80948d_1    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pillow                    9.0.1            py39hae2aec6_2    conda-forge
pip                       22.0.3             pyhd8ed1ab_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge
python                    3.9.10          h85951f9_2_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
sander                    16.0                     pypi_0    pypi
scipy                     1.8.0            py39hee8e79c_1    conda-forge
setuptools                60.9.3           py39hf3d152e_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.37.0               h9cd32fc_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tzdata                    2021e                he74cb21_0    conda-forge
unicodedata2              14.0.0           py39h3811e60_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge

Details about conda and system ( conda info ):

     active environment : conda_at21
    active env location : /home/mario/programs/miniconda3.9/envs/conda_at21
            shell level : 1
       user config file : /home/mario/.condarc
 populated config files : /home/mario/.condarc
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.9.1.final.0
       virtual packages : __cuda=11.6=0
                          __linux=5.4.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/mario/programs/miniconda3.9  (writable)
      conda av data dir : /home/mario/programs/miniconda3.9/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/mario/programs/miniconda3.9/pkgs
                          /home/mario/.conda/pkgs
       envs directories : /home/mario/programs/miniconda3.9/envs
                          /home/mario/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.1 Linux/5.4.0-100-generic linuxmint/20.2 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

osx builds?

Thanks for maintaining a conda-forge build of AmberTools!

Has there been an effort to build osx builds of this feedstock? If not, I wonder if @hainm has some thoughts on how we might be able to get that to work.

Locally build the conda package in an OSX platform

Comment:

Hi, I wonder if you guys have any experience with regard to do a local build of the OSX-64 conda package?
I have been using build-locally.py script to build the package for linux-64 on a linux machine and it worked fine.
But if I tried to do the same thing on my MacOS laptop, I got the following error.

-- The C compiler identification is Clang 15.0.7
-- The CXX compiler identification is Clang 15.0.7
-- The Fortran compiler identification is GNU 12.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - failed
-- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - broken
CMake Error at /Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_build_env/share/cmake-3.20/Modules/CMakeTestCCompiler.cmake:66 (message):
  The C compiler

    "/Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_build_env/bin/x86_64-apple-darwin13.4.0-clang"

  is not able to compile a simple test program.

  It fails with the following output:

    Change Dir: /Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/work/build/CMakeFiles/CMakeTmp
    
    Run Build Command(s):/Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_build_env/bin/make -f Makefile cmTC_f9850/fast && /Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_build_env/bin/make  -f CMakeFiles/cmTC_f9850.dir/build.make CMakeFiles/cmTC_f9850.dir/build
    make[1]: Entering directory '/Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/work/build/CMakeFiles/CMakeTmp'
    Building C object CMakeFiles/cmTC_f9850.dir/testCCompiler.c.o
    /Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_build_env/bin/x86_64-apple-darwin13.4.0-clang   -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/include -fdebug-prefix-map=/Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/work=/usr/local/src/conda/ambertools-23.3 -fdebug-prefix-map=/Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p=/usr/local/src/conda-prefix  -arch x86_64 -mmacosx-version-min=10.9 -MD -MT CMakeFiles/cmTC_f9850.dir/testCCompiler.c.o -MF CMakeFiles/cmTC_f9850.dir/testCCompiler.c.o.d -o CMakeFiles/cmTC_f9850.dir/testCCompiler.c.o -c /Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/work/build/CMakeFiles/CMakeTmp/testCCompiler.c
    Linking C executable cmTC_f9850
    /Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_build_env/bin/cmake -E cmake_link_script CMakeFiles/cmTC_f9850.dir/link.txt --verbose=1
    /Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_build_env/bin/x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/include -fdebug-prefix-map=/Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/work=/usr/local/src/conda/ambertools-23.3 -fdebug-prefix-map=/Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p=/usr/local/src/conda-prefix  -arch x86_64 -mmacosx-version-min=10.9 -Wl,-search_paths_first -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -L/Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib  CMakeFiles/cmTC_f9850.dir/testCCompiler.c.o -o cmTC_f9850 
    ld: library not found for -lSystem
    clang-15: error: linker command failed with exit code 1 (use -v to see invocation)
    make[1]: *** [CMakeFiles/cmTC_f9850.dir/build.make:100: cmTC_f9850] Error 1
    make[1]: Leaving directory '/Users/zwu/src/amber-feedstock/miniforge3/conda-bld/ambertools_1698769639923/work/build/CMakeFiles/CMakeTmp'
    make: *** [Makefile:127: cmTC_f9850/fast] Error 2

MPI builds

Comment:

It seems to me that MPI is not enabled in this recipe. I'd like to know if there is any specific reason for it, or if I can contribute to enable MPI.

Build versions published since 20.9

List of pending patches:

• 20.9 - check #50 - CI report
• 20.10 - check #53 - CI report
• 20.11 - check #54 - CI report
• 20.12 - check #55 - CI report
• 20.13 - check #56 - CI report
• 20.14 - check #57 - CI report

Note that the PPC builds time out very often so it's tricky to get them uploaded. Many retries needed. If you don't see a particular package online, check the CI report for that version.

Version should include minor version number

I noticed that this package is listed as version 19, without minor or bugfix releases.

The official AMBER conda distribution includes a minor version number because typically multiple patch versions are released during the lifecycle of AmberTools to either add new features or fix bugs. Since Amber ff19SB was just released, it seems very likely that there will be more releases during the lifecycle of AmberTools 19, so it may be good to include this minor version number---if at least for consistency!

OSX builds do not include xleap and other GUIs

Due to incompatibilities between tk and xorg-*, osx packages can't build graphical interfaces such as xleap. We will keep an eye on this area and update accordingly.

Can't find `ambertools` on conda-forge

Unless I'm making a typo that I can't find, it seems amber tools is not properly listed on conda-forge. (Aside from directly searching, like below, I also can't install ambertools if list conda-forge as a channel in an environment YAML file.)

$ conda search ambertools --channel conda-forge
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Loading channels: done
No match found for: ambertools. Search: *ambertools*

PackagesNotFoundError: The following packages are not available from current channels:

  - ambertools

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Environment (conda list):

$ conda list
WARNING: The conda.compat module is deprecated and will be removed in a future release.
# packages in environment at /anaconda3:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0
alabaster                 0.7.12                   py37_0
anaconda                  2019.03                  py37_0
anaconda-client           1.7.2                    py37_0
anaconda-navigator        1.9.7                    py37_0
anaconda-project          0.8.2                    py37_0
appnope                   0.1.0                    py37_0
appscript                 1.1.0            py37h1de35cc_0
argh                      0.26.2                   pypi_0    pypi
asn1crypto                0.24.0                   py37_0
astroid                   2.2.5                    py37_0
astropy                   3.1.2            py37h1de35cc_0
atomicwrites              1.3.0                    py37_1
attrs                     19.1.0                   py37_1
babel                     2.6.0                    py37_0
backcall                  0.1.0                    py37_0
backports                 1.0                      py37_1
backports.os              0.1.1                    py37_0
backports.shutil_get_terminal_size 1.0.0                    py37_2
beautifulsoup4            4.7.1                    py37_1
bitarray                  0.8.3            py37h1de35cc_0
bkcharts                  0.2                      py37_0
blas                      1.0                         mkl
bleach                    3.1.0                    py37_0
blosc                     1.15.0               hd9629dc_0
bokeh                     1.0.4                    py37_0
boto                      2.49.0                   py37_0
bottleneck                1.2.1            py37h1d22016_1
bzip2                     1.0.6                h1de35cc_5
ca-certificates           2019.1.23                     0
certifi                   2019.3.9                 py37_0
cffi                      1.12.2           py37hb5b8e2f_1
chardet                   3.0.4                    py37_1
click                     7.0                      py37_0
cloudpickle               0.8.0                    py37_0
clyent                    1.2.2                    py37_1
colorama                  0.4.1                    py37_0
conda                     4.6.11                   py37_0
conda-build               3.17.8                   py37_0
conda-env                 2.6.0                         1
conda-verify              3.1.1                    py37_0
contextlib2               0.5.5                    py37_0
cryptography              2.6.1            py37ha12b0ac_0
curl                      7.64.0               ha441bb4_2
cycler                    0.10.0                   py37_0
cython                    0.29.6           py37h0a44026_0
cytoolz                   0.9.0.1          py37h1de35cc_1
dask                      1.1.4                    py37_1
dask-core                 1.1.4                    py37_1
dbus                      1.13.6               h90a0687_0
decorator                 4.4.0                    py37_1
defusedxml                0.5.0                    py37_1
distributed               1.26.0                   py37_1
docutils                  0.14                     py37_0
entrypoints               0.3                      py37_0
errorhandler              2.0.1                    pypi_0    pypi
et_xmlfile                1.0.1                    py37_0
expat                     2.2.6                h0a44026_0
fastcache                 1.0.2            py37h1de35cc_2
filelock                  3.0.10                   py37_0
flask                     1.0.2                    py37_1
freetype                  2.9.1                hb4e5f40_0
future                    0.17.1                   py37_0
get_terminal_size         1.0.0                h7520d66_0
gettext                   0.19.8.1             h15daf44_3
gevent                    1.4.0            py37h1de35cc_0
glib                      2.56.2               hd9629dc_0
glob2                     0.6                      py37_1
gmp                       6.1.2                hb37e062_1
gmpy2                     2.0.8            py37h6ef4df4_2
greenlet                  0.4.15           py37h1de35cc_0
h5py                      2.9.0            py37h3134771_0
hdf5                      1.10.4               hfa1e0ec_0
heapdict                  1.0.0                    py37_2
html5lib                  1.0.1                    py37_0
icu                       58.2                 h4b95b61_1
idna                      2.8                      py37_0
imageio                   2.5.0                    py37_0
imagesize                 1.1.0                    py37_0
importlib_metadata        0.8                      py37_0
intel-openmp              2019.3                      199
ipykernel                 5.1.0            py37h39e3cac_0
ipython                   7.4.0            py37h39e3cac_0
ipython_genutils          0.2.0                    py37_0
ipywidgets                7.4.2                    py37_0
isbnlib                   3.9.8                    pypi_0    pypi
isort                     4.3.16                   py37_0
itsdangerous              1.1.0                    py37_0
jbig                      2.1                  h4d881f8_0
jdcal                     1.4                      py37_0
jedi                      0.13.3                   py37_0
jinja2                    2.10                     py37_0
jpeg                      9b                   he5867d9_2
jsonref                   0.2                      pypi_0    pypi
jsonschema                3.0.1                    py37_0
jupyter                   1.0.0                    py37_7
jupyter_client            5.2.4                    py37_0
jupyter_console           6.0.0                    py37_0
jupyter_core              4.4.0                    py37_0
jupyterlab                0.35.4           py37hf63ae98_0
jupyterlab_server         0.2.0                    py37_0
keyring                   18.0.0                   py37_0
kiwisolver                1.0.1            py37h0a44026_0
krb5                      1.16.1               hddcf347_7
lazy-object-proxy         1.3.1            py37h1de35cc_2
libarchive                3.3.3                h786848e_5
libcurl                   7.64.0               h051b688_2
libcxx                    4.0.1                hcfea43d_1
libcxxabi                 4.0.1                hcfea43d_1
libedit                   3.1.20181209         hb402a30_0
libffi                    3.2.1                h475c297_4
libgfortran               3.0.1                h93005f0_2
libiconv                  1.15                 hdd342a3_7
liblief                   0.9.0                h2a1bed3_2
libpng                    1.6.36               ha441bb4_0
libsodium                 1.0.16               h3efe00b_0
libssh2                   1.8.0                ha12b0ac_4
libtiff                   4.0.10               hcb84e12_2
libxml2                   2.9.9                hab757c2_0
libxslt                   1.1.33               h33a18ac_0
llvmlite                  0.28.0           py37h8c7ce04_0
locket                    0.2.0                    py37_1
lxml                      4.3.2            py37hef8c89e_0
lz4-c                     1.8.1.2              h1de35cc_0
lzo                       2.10                 h362108e_2
manubot                   0.2.4                    pypi_0    pypi
markupsafe                1.1.1            py37h1de35cc_0
matplotlib                3.0.3            py37h54f8f79_0
mccabe                    0.6.1                    py37_1
mistune                   0.8.4            py37h1de35cc_0
mkl                       2019.3                      199
mkl-service               1.1.2            py37hfbe908c_5
mkl_fft                   1.0.10           py37h5e564d8_0
mkl_random                1.0.2            py37h27c97d8_0
more-itertools            6.0.0                    py37_0
mpc                       1.1.0                h6ef4df4_1
mpfr                      4.0.1                h3018a27_3
mpmath                    1.1.0                    py37_0
msgpack-python            0.6.1            py37h04f5b5a_1
multipledispatch          0.6.0                    py37_0
navigator-updater         0.2.1                    py37_0
nbconvert                 5.4.1                    py37_3
nbformat                  4.4.0                    py37_0
ncurses                   6.1                  h0a44026_1
networkx                  2.2                      py37_1
nltk                      3.4                      py37_1
nose                      1.3.7                    py37_2
notebook                  5.7.8                    py37_0
numba                     0.43.1           py37h6440ff4_0
numexpr                   2.6.9            py37h7413580_0
numpy                     1.16.2           py37hacdab7b_0
numpy-base                1.16.2           py37h6575580_0
numpydoc                  0.8.0                    py37_0
olefile                   0.46                     py37_0
openpyxl                  2.6.1                    py37_1
openssl                   1.1.1b               h1de35cc_1
packaging                 19.0                     py37_0
pandas                    0.24.2           py37h0a44026_0
pandoc                    2.2.3.2                       0
pandoc-eqnos              1.4.3                    pypi_0    pypi
pandoc-fignos             1.4.2                    pypi_0    pypi
pandoc-tablenos           1.4.2                    pypi_0    pypi
pandoc-xnos               1.2.0                    pypi_0    pypi
pandocfilters             1.4.2                    py37_1
parso                     0.3.4                    py37_0
partd                     0.3.10                   py37_1
path.py                   11.5.0                   py37_0
pathlib2                  2.3.3                    py37_0
pathtools                 0.1.2                    pypi_0    pypi
patsy                     0.5.1                    py37_0
pcre                      8.43                 h0a44026_0
pep8                      1.7.1                    py37_0
pexpect                   4.6.0                    py37_0
pickleshare               0.7.5                    py37_0
pillow                    5.4.1            py37hb68e598_0
pip                       19.0.3                   py37_0
pkginfo                   1.5.0.1                  py37_0
pluggy                    0.9.0                    py37_0
ply                       3.11                     py37_0
prometheus_client         0.6.0                    py37_0
prompt_toolkit            2.0.9                    py37_0
psutil                    5.6.1            py37h1de35cc_0
ptyprocess                0.6.0                    py37_0
py                        1.8.0                    py37_0
py-lief                   0.9.0            py37h1413db1_2
pybase62                  0.4.0                    pypi_0    pypi
pycodestyle               2.5.0                    py37_0
pycosat                   0.6.3            py37h1de35cc_0
pycparser                 2.19                     py37_0
pycrypto                  2.6.1            py37h1de35cc_9
pycurl                    7.43.0.2         py37ha12b0ac_0
pyflakes                  2.1.1                    py37_0
pygments                  2.3.1                    py37_0
pylint                    2.3.1                    py37_0
pyodbc                    4.0.26           py37h0a44026_0
pyopenssl                 19.0.0                   py37_0
pyparsing                 2.3.1                    py37_0
pyqt                      5.9.2            py37h655552a_2
pyrsistent                0.14.11          py37h1de35cc_0
pysocks                   1.6.8                    py37_0
pytables                  3.5.1            py37h5bccee9_0
pytest                    4.3.1                    py37_0
pytest-arraydiff          0.3              py37h39e3cac_0
pytest-astropy            0.5.0                    py37_0
pytest-doctestplus        0.3.0                    py37_0
pytest-openfiles          0.3.2                    py37_0
pytest-remotedata         0.3.1                    py37_0
python                    3.7.3                h359304d_0
python-dateutil           2.8.0                    py37_0
python-libarchive-c       2.8                      py37_6
python.app                2                        py37_9
pytz                      2018.9                   py37_0
pywavelets                1.0.2            py37h1d22016_0
pyyaml                    5.1              py37h1de35cc_0
pyzmq                     18.0.0           py37h0a44026_0
qt                        5.9.7                h468cd18_1
qtawesome                 0.5.7                    py37_1
qtconsole                 4.4.3                    py37_0
qtpy                      1.7.0                    py37_1
ratelimiter               1.2.0.post0              pypi_0    pypi
readline                  7.0                  h1de35cc_5
requests                  2.21.0                   py37_0
requests-cache            0.5.0                    pypi_0    pypi
rope                      0.12.0                   py37_0
ruamel_yaml               0.15.46          py37h1de35cc_0
scikit-image              0.14.2           py37h0a44026_0
scikit-learn              0.20.3           py37h27c97d8_0
scipy                     1.2.1            py37h1410ff5_0
seaborn                   0.9.0                    py37_0
send2trash                1.5.0                    py37_0
setuptools                40.8.0                   py37_0
simplegeneric             0.8.1                    py37_2
singledispatch            3.4.0.3                  py37_0
sip                       4.19.8           py37h0a44026_0
six                       1.12.0                   py37_0
snappy                    1.1.7                he62c110_3
snowballstemmer           1.2.1                    py37_0
sortedcollections         1.1.2                    py37_0
sortedcontainers          2.1.0                    py37_0
soupsieve                 1.8                      py37_0
sphinx                    1.8.5                    py37_0
sphinxcontrib             1.0                      py37_1
sphinxcontrib-websupport  1.1.0                    py37_1
spyder                    3.3.3                    py37_0
spyder-kernels            0.4.2                    py37_0
sqlalchemy                1.3.1            py37h1de35cc_0
sqlite                    3.27.2               ha441bb4_0
statsmodels               0.9.0            py37h1d22016_0
sympy                     1.3                      py37_0
tblib                     1.3.2                    py37_0
terminado                 0.8.1                    py37_1
testpath                  0.4.2                    py37_0
tk                        8.6.8                ha441bb4_0
toolz                     0.9.0                    py37_0
tornado                   6.0.2            py37h1de35cc_0
tqdm                      4.31.1                   py37_1
traitlets                 4.3.2                    py37_0
unicodecsv                0.14.1                   py37_0
unixodbc                  2.3.7                h1de35cc_0
urllib3                   1.24.1                   py37_0
watchdog                  0.9.0                    pypi_0    pypi
wcwidth                   0.1.7                    py37_0
webencodings              0.5.1                    py37_1
werkzeug                  0.14.1                   py37_0
wheel                     0.33.1                   py37_0
widgetsnbextension        3.4.2                    py37_0
wrapt                     1.11.1           py37h1de35cc_0
wurlitzer                 1.0.2                    py37_0
xlrd                      1.2.0                    py37_0
xlsxwriter                1.1.5                    py37_0
xlwings                   0.15.4                   py37_0
xlwt                      1.3.0                    py37_0
xz                        5.2.4                h1de35cc_4
yaml                      0.1.7                hc338f04_2
zeromq                    4.3.1                h0a44026_3
zict                      0.1.4                    py37_0
zipp                      0.3.3                    py37_1
zlib                      1.2.11               h1de35cc_3
zstd                      1.3.7                h5bba6e5_0

Details about conda and system ( conda info ):

$ conda info

     active environment : base
    active env location : /anaconda3
            shell level : 1
       user config file : /Users/dslochower/.condarc
 populated config files :
          conda version : 4.6.11
    conda-build version : 3.17.8
         python version : 3.7.3.final.0
       base environment : /anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /anaconda3/pkgs
                          /Users/dslochower/.conda/pkgs
       envs directories : /anaconda3/envs
                          /Users/dslochower/.conda/envs
               platform : osx-64
             user-agent : conda/4.6.11 requests/2.21.0 CPython/3.7.3 Darwin/18.6.0 OSX/10.14.5
                UID:GID : 501:20
             netrc file : None
           offline mode : False

MMGBSA.py can not find 'alamdcrd' module

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

1. Create an environment containing ambertools:

$ conda create -n test -c conda-forge ambertools

2. Run MMPBSA.py

$ MMPBSA.py -O -i mmpbsa.in -o mmpbsa.out -sp wat.prmtop -cp wat%strip.prmtop -rp rec.prmtop -lp lig.prmtop -y prod.nc
Loading and checking parameter files for compatibility...
cpptraj found! Using /home/zhesheng/.conda/envs/test/bin/cpptraj
mmpbsa_py_energy found! Using /home/zhesheng/.conda/envs/test/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
  File "/home/zhesheng/.conda/envs/test/bin/MMPBSA.py", line 4, in <module>
    __import__('pkg_resources').run_script('MMPBSA.py==16.0', 'MMPBSA.py')
  File "/home/zhesheng/.conda/envs/test/lib/python3.9/site-packages/pkg_resources/__init__.py", line 662, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/zhesheng/.conda/envs/test/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1466, in run_script
    exec(script_code, namespace, namespace)
  File "/home/zhesheng/.conda/envs/test/lib/python3.9/site-packages/MMPBSA.py-16.0-py3.9.egg/EGG-INFO/scripts/MMPBSA.py", line 99, in <module>
  File "/home/zhesheng/.conda/envs/test/lib/python3.9/site-packages/MMPBSA.py-16.0-py3.9.egg/MMPBSA_mods/main.py", line 167, in file_setup
    self.mut_str, mutant_residue = make_mutant_trajectories(INPUT, FILES,
  File "/home/zhesheng/.conda/envs/test/lib/python3.9/site-packages/MMPBSA.py-16.0-py3.9.egg/MMPBSA_mods/make_trajs.py", line 298, in make_mutant_trajectories
    from alamdcrd import MutantMdcrd, GlyMutantMdcrd
ModuleNotFoundError: No module named 'alamdcrd'

Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.

3. Failed with "No module named 'alamdcrd'"

Installed packages

# packages in environment at /home/zhesheng/.conda/envs/test:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    conda-forge
ambertools                21.12            py39hc630cb1_0    conda-forge
amberutils                21.0                     pypi_0    pypi
arpack                    3.7.0                hdefa2d7_2    conda-forge
blas                      2.106                  openblas    conda-forge
boost-cpp                 1.74.0               hc6e9bd1_3    conda-forge
bottleneck                1.3.4            py39hce1f21e_0
brotli                    1.0.9                he6710b0_2
bzip2                     1.0.8                h7b6447c_0
c-ares                    1.18.1               h7f8727e_0
ca-certificates           2022.3.29            h06a4308_1
certifi                   2021.10.8        py39h06a4308_2
curl                      7.82.0               h7f8727e_0
cycler                    0.11.0             pyhd3eb1b0_0
cython                    0.29.28          py39h295c915_0
fftw                      3.3.10          nompi_h77c792f_102    conda-forge
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.11.0               h70c0345_0
giflib                    5.2.1                h7b6447c_0
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.12.1          nompi_h2386368_104    conda-forge
icu                       68.1                 h2531618_0
jpeg                      9d                   h7f8727e_0
kiwisolver                1.3.2            py39h295c915_0
krb5                      1.19.2               hac12032_0
lcms2                     2.12                 h3be6417_0
ld_impl_linux-64          2.35.1               h7274673_9
libblas                   3.9.0                6_openblas    conda-forge
libcblas                  3.9.0                6_openblas    conda-forge
libcurl                   7.82.0               h0b77cf5_0
libedit                   3.1.20210910         h7f8727e_0
libev                     4.33                 h7f8727e_1
libffi                    3.3                  he6710b0_2
libgcc-ng                 11.2.0              h1d223b6_16    conda-forge
libgfortran-ng            11.2.0              h69a702a_16    conda-forge
libgfortran5              11.2.0              h5c6108e_16    conda-forge
libgomp                   11.2.0              h1d223b6_16    conda-forge
liblapack                 3.9.0                6_openblas    conda-forge
liblapacke                3.9.0                6_openblas    conda-forge
libnetcdf                 4.8.1           nompi_hb3fd0d9_101    conda-forge
libnghttp2                1.46.0               hce63b2e_0
libopenblas               0.3.12          pthreads_h4812303_1    conda-forge
libpng                    1.6.37               hbc83047_0
libssh2                   1.9.0                h1ba5d50_1
libstdcxx-ng              11.2.0              he4da1e4_16    conda-forge
libtiff                   4.2.0                h85742a9_0
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp                   1.2.2                h55f646e_0
libwebp-base              1.2.2                h7f8727e_0
libxcb                    1.14                 h7b6447c_0
libzip                    1.8.0                h4de3113_1    conda-forge
libzlib                   1.2.11            h166bdaf_1014    conda-forge
llvm-openmp               13.0.1               he0ac6c6_1    conda-forge
lz4-c                     1.9.3                h295c915_1
matplotlib-base           3.5.1            py39ha18d171_1
munkres                   1.1.4                      py_0
ncurses                   6.3                  h7f8727e_2
netcdf-fortran            4.5.4           nompi_h2b6e579_100    conda-forge
numexpr                   2.8.1            py39hecfb737_0
numpy                     1.21.5           py39h7a5d4dd_1
numpy-base                1.21.5           py39hb8be1f0_1
openssl                   1.1.1n               h7f8727e_0
packaging                 21.3               pyhd3eb1b0_0
packmol                   20.010               h86c2bf4_0    conda-forge
packmol-memgen            1.2.1rc0                 pypi_0    pypi
pandas                    1.4.2            py39h295c915_0
parmed                    3.4.3            py39h5a03fae_2    conda-forge
perl                      5.26.2               h14c3975_0
pillow                    9.0.1            py39h22f2fdc_0
pip                       21.2.4           py39h06a4308_0
pyparsing                 3.0.4              pyhd3eb1b0_0
python                    3.9.12               h12debd9_0
python-dateutil           2.8.2              pyhd3eb1b0_0
python_abi                3.9                      2_cp39    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2021.3             pyhd3eb1b0_0
readline                  8.1.2                h7f8727e_1
sander                    16.0                     pypi_0    pypi
scipy                     1.8.0            py39hee8e79c_1    conda-forge
setuptools                61.2.0           py39h06a4308_0
six                       1.16.0             pyhd3eb1b0_1
sqlite                    3.38.2               hc218d9a_0
tk                        8.6.11               h1ccaba5_0
tzdata                    2022a                hda174b7_0
wheel                     0.37.1             pyhd3eb1b0_0
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h27cfd23_1007
xz                        5.2.5                h7b6447c_0
zlib                      1.2.11            h166bdaf_1014    conda-forge
zstd                      1.4.9                haebb681_0

Environment info

active environment : test
    active env location : /home/zhesheng/.conda/envs/test
            shell level : 1
       user config file : /home/zhesheng/.condarc
 populated config files : /home/zhesheng/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.7.final.0
       virtual packages : __linux=4.18.0=0
                          __glibc=2.28=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/zhesheng/.conda  (read only)
      conda av data dir : /home/zhesheng/.conda/etc/conda
  conda av metadata url : None
           channel URLs : https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/linux-64
                          https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/noarch
                          https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/linux-64
                          https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/noarch
          package cache : /home/zhesheng/.conda/pkgs
       envs directories : /home/zhesheng/.conda/envs
               platform : linux-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.7 Linux/4.18.0-305.el8.x86_64 rhel/8.4 glibc/2.28
                UID:GID : 40041:40006
             netrc file : None
           offline mode : False

ParmEd 4.0.0 pin preventing bot migration

Comment:

ParmEd as a dependency is hard pinned to 4.0.0 from #102, but only newer versions (4.2.2+) support Python 3.12. This is preventing the bot from attempting a migration. Here's a run and relevant bits of log are below.

Can we loosen this to parmed =4?

                linux_64_numpy1.26python3.12.____cpython: Could not solve for environment specs
The following packages are incompatible
├─ parmed 4.0.0.*  is installable with the potential options
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.10.* *_cp310, which can be installed;
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.11.* *_cp311, which can be installed;
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.8.* *_cp38, which can be installed;
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.8 *_pypy38_pp73, which can be installed;
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.9.* *_cp39, which can be installed;
│  └─ parmed 4.0.0 would require
│     └─ python_abi 3.9 *_pypy39_pp73, which can be installed;
└─ python 3.12.* *_cpython is not installable because there are no viable options
   ├─ python 3.12.0 would require
   │  └─ python_abi 3.12.* *_cp312, which conflicts with any installable versions previously reported;
   └─ python 3.12.0rc3 would require
      └─ _python_rc, which does not exist (perhaps a missing channel).
osx_64_numpy1.26python3.12.____cpython: Could not solve for environment specs
The following packages are incompatible
├─ parmed 4.0.0.*  is installable with the potential options
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.10.* *_cp310, which can be installed;
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.11.* *_cp311, which can be installed;
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.8 *_pypy38_pp73, which can be installed;
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.8.* *_cp38, which can be installed;
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.9.* *_cp39, which can be installed;
│  └─ parmed 4.0.0 would require
│     └─ python_abi 3.9 *_pypy39_pp73, which can be installed;
└─ python 3.12.* *_cpython is not installable because there are no viable options
   ├─ python 3.12.0 would require
   │  └─ python_abi 3.12.* *_cp312, which conflicts with any installable versions previously reported;
   └─ python 3.12.0rc3 would require
      └─ _python_rc, which does not exist (perhaps a missing channel).
osx_arm64_numpy1.26python3.12.____cpython: Could not solve for environment specs
The following packages are incompatible
├─ parmed 4.0.0.*  is installable with the potential options
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.10.* *_cp310, which can be installed;
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.11.* *_cp311, which can be installed;
│  ├─ parmed 4.0.0 would require
│  │  └─ python_abi 3.8.* *_cp38, which can be installed;
│  └─ parmed 4.0.0 would require
│     └─ python_abi 3.9.* *_cp39, which can be installed;
└─ python 3.12.* *_cpython is not installable because there are no viable options
   ├─ python 3.12.0 would require
   │  └─ python_abi 3.12.* *_cp312, which conflicts with any installable versions previously reported;
   └─ python 3.12.0rc3 would require
      └─ _python_rc, which does not exist (perhaps a missing channel).

Ambertools should depend on ParmEd

Instead of bundling ParmEd with AmberTools, add the already existing package to the requirements, so downstream packages can use both if needed without clobbering issues (e.g. omnia-md/conda-recipes#1011 (comment)).

PowerPC builds?

Hi, could it be possible to obtain ppc64le builds for this package?

I have checked the host requirements and some do not have a PowerPC package yet, though. Namely:

• openmp is not needed! osx requires llvmp-openmp
• bc - Submitted PR here. Tests are passing, we are now waiting for review.
• tcsh - Submitted PR here. Tests are passing, we are now waiting for review.

Thanks!

Run test suite on CI

We could create a PR to simply run the tests on the CI machinery, thus testing all target platforms.

For reference, we might need to generate a fake config.h as suggested in https://github.com/Amber-MD/cmake-buildscripts/issues/85#issuecomment-338851577. We can benefit from CB env variables to parametrize the file:

INSTALLTYPE=serial
AMBER_SOURCE=/Users/haichit/amber_git/amber
AMBER_PREFIX=/Users/haichit/amber_git/cmake/tmp
BINDIR=/Users/haichit/amber_git/cmake/tmp/bin
DATDIR=/Users/haichit/amber_git/cmake/tmp/dat
LIBDIR=/Users/haichit/amber_git/cmake/tmp/lib
INCDIR=/Users/haichit/amber_git/cmake/tmp/include
PYTHON=python
SKIP_PYTHON=no
SHARED_SUFFIX=.dylib

I'll leave this here as a reminder. First we need osx to build 💪

Pending updates

• #98
• #99
• #100
• #101

Package reports version 17, even though it's 20

Issue: Installing the latest package has conda list reporting version 17.0 and source pypi. I think I recall this being a consequence of the internal bundling of miniconda, but it would help with debugging if we could get the package version reported correctly.

(I know Jaime just headed out for a two week vacation -- I'm doing the same for the next week, just wanted to jot this down somewhere)

$ conda list | grep amber

amberlite                 16.0                     pypi_0    pypi
ambertools                17.0                     pypi_0    pypi
pdb4amber                 1.7.dev0                 pypi_0    pypi

Environment (conda list):

(off-dev) jeffreywagner@JW-MBP$ conda list
# packages in environment at /Users/jeffreywagner/miniconda3/envs/off-dev:
#
# Name                    Version                   Build  Channel
abseil-cpp                20200225.2           h4a8c4bd_0    conda-forge
alabaster                 0.7.12                     py_0    conda-forge
amberlite                 16.0                     pypi_0    pypi
ambertools                17.0                     pypi_0    pypi
apbs                      1.5                  h1de35cc_3    schrodinger
appnope                   0.1.0           py37hc8dfbb8_1001    conda-forge
arpack                    3.7.0                hbb27dc6_1    conda-forge
arrow-cpp                 0.17.1          py37h898ce22_2_cpu    conda-forge
attrs                     19.3.0                     py_0    conda-forge
aws-sdk-cpp               1.7.164              h5c602de_1    conda-forge
babel                     2.8.0                      py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
biopython                 1.76             py37h0b31af3_0    conda-forge
bleach                    3.1.4              pyh9f0ad1d_0    conda-forge
boost                     1.72.0           py37hbf1eeb5_0    conda-forge
boost-cpp                 1.72.0               hdf9ef73_0    conda-forge
brotli                    1.0.7             h4a8c4bd_1001    conda-forge
brotlipy                  0.7.0           py37h9bfed18_1000    conda-forge
bson                      0.5.9                      py_0    conda-forge
bzip2                     1.0.8                h0b31af3_2    conda-forge
c-ares                    1.15.0            h01d97ff_1001    conda-forge
ca-certificates           2020.6.20            hecda079_0    conda-forge
cairo                     1.16.0            hec6a9b0_1003    conda-forge
certifi                   2020.6.20        py37hc8dfbb8_0    conda-forge
cffi                      1.14.0           py37h356ff06_0    conda-forge
cftime                    1.1.3            py37h10e2902_0    conda-forge
chardet                   3.0.4           py37hc8dfbb8_1006    conda-forge
codecov                   2.1.5              pyh9f0ad1d_0    conda-forge
coverage                  5.1              py37h9bfed18_0    conda-forge
cryptography              2.8              py37he655712_2    conda-forge
curl                      7.69.1               h2d98d24_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
cython                    0.29.16          py37h570ac47_0    conda-forge
dbus                      1.13.6               h2f22bb5_0    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
docutils                  0.16             py37hc8dfbb8_1    conda-forge
entrypoints               0.3             py37hc8dfbb8_1001    conda-forge
expat                     2.2.9                h4a8c4bd_2    conda-forge
fftw                      3.3.8           nompi_h44ae4c8_1110    conda-forge
fftw3f                    3.3.4                         2    omnia
fontconfig                2.13.1            h6b1039f_1001    conda-forge
freemol                   1.158                      py_2    schrodinger
freetype                  2.10.1               h8da9a1a_0    conda-forge
gettext                   0.19.8.1          h46ab8bc_1002    conda-forge
gflags                    2.2.2             h4a8c4bd_1002    conda-forge
glew                      2.0.0                         0    schrodinger
glib                      2.64.2               h577aef8_0    conda-forge
glog                      0.4.0                h700f914_3    conda-forge
griddataformats           0.5.0                      py_0    conda-forge
grpc-cpp                  1.29.0               h0284957_0    conda-forge
gsd                       2.1.1            py37h10e2902_0    conda-forge
h5py                      2.10.0          nompi_py37h106b333_102    conda-forge
hdf4                      4.2.13            h84186c3_1003    conda-forge
hdf5                      1.10.5          nompi_h3e39495_1104    conda-forge
icu                       64.2                 h6de7cb9_1    conda-forge
idna                      2.9                        py_1    conda-forge
imagesize                 1.2.0                      py_0    conda-forge
importlib-metadata        1.6.0            py37hc8dfbb8_0    conda-forge
importlib_metadata        1.6.0                         0    conda-forge
ipykernel                 5.2.1            py37h43977f1_0    conda-forge
ipython                   7.13.0           py37hc8dfbb8_2    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.5.1                      py_0    conda-forge
jedi                      0.17.0           py37hc8dfbb8_0    conda-forge
jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
joblib                    0.15.1                     py_0    conda-forge
jpeg                      9c                h1de35cc_1001    conda-forge
jsonschema                3.2.0            py37hc8dfbb8_1    conda-forge
jupyter_client            6.1.3                      py_0    conda-forge
jupyter_core              4.6.3            py37hc8dfbb8_1    conda-forge
kiwisolver                1.2.0            py37ha1cc60f_0    conda-forge
krb5                      1.17.1               h1752a42_0    conda-forge
libblas                   3.8.0               16_openblas    conda-forge
libcblas                  3.8.0               16_openblas    conda-forge
libcurl                   7.69.1               hc0b9707_0    conda-forge
libcxx                    10.0.0                        1    conda-forge
libedit                   3.1.20191231         hed1e85f_0    conda-forge
libevent                  2.1.10               hafa8578_0    conda-forge
libffi                    3.2.1             h4a8c4bd_1007    conda-forge
libgfortran               4.0.0                         2    conda-forge
libiconv                  1.15              h0b31af3_1006    conda-forge
liblapack                 3.8.0               16_openblas    conda-forge
libllvm9                  9.0.1                h7475705_1    conda-forge
libnetcdf                 4.7.4           nompi_he461dc0_101    conda-forge
libopenblas               0.3.9                h3d69b6c_0    conda-forge
libpng                    1.6.37               hbbe82c9_1    conda-forge
libpq                     12.2                 h489d428_1    conda-forge
libprotobuf               3.11.4               hd174df1_0    conda-forge
libsodium                 1.0.17               h01d97ff_0    conda-forge
libssh2                   1.8.2                hcdc9a53_2    conda-forge
libtiff                   4.1.0                h2ae36a8_6    conda-forge
libwebp-base              1.1.0                h0b31af3_3    conda-forge
libxcb                    1.13              h1de35cc_1002    conda-forge
libxml2                   2.9.10               h53d96d6_0    conda-forge
libxslt                   1.1.33               h320ff13_0    conda-forge
llvm-openmp               10.0.0               h28b9765_0    conda-forge
lxml                      4.5.1            py37heb1707f_0    conda-forge
lz4-c                     1.9.2                h4a8c4bd_0    conda-forge
m2r                       0.2.1                      py_0    conda-forge
m2rr                      0.2.3                    pypi_0    pypi
markupsafe                1.1.1            py37h9bfed18_1    conda-forge
matplotlib                3.2.1                         0    conda-forge
matplotlib-base           3.2.1            py37hddda452_0    conda-forge
mdanalysis                0.20.1           py37h4a8c4bd_0    conda-forge
mengine                   1                    h1de35cc_1    schrodinger
mistune                   0.8.4           py37h9bfed18_1001    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
mmtf-python               1.1.2                      py_0    conda-forge
more-itertools            8.2.0                      py_0    conda-forge
mpeg_encode               1                    h1de35cc_1    schrodinger
msgpack-python            1.0.0            py37ha1cc60f_1    conda-forge
mtz2ccp4_px               1.0                  hdc02c5d_3    schrodinger
nbconvert                 5.6.1            py37hc8dfbb8_1    conda-forge
nbformat                  5.0.6                      py_0    conda-forge
nbsphinx                  0.7.0              pyh9f0ad1d_0    conda-forge
ncurses                   6.1               h0a44026_1002    conda-forge
netcdf-fortran            4.5.2           nompi_h0361502_104    conda-forge
netcdf4                   1.5.3           nompi_py37h19ea5d6_103    conda-forge
networkx                  2.4                        py_1    conda-forge
nglview                   2.7.5              pyh5ca1d4c_0    conda-forge
notebook                  6.0.3                    py37_0    conda-forge
nspr                      4.20              h0a44026_1000    conda-forge
nss                       3.47                 hc0980d9_0    conda-forge
numpy                     1.18.1           py37h7687784_1    conda-forge
numpydoc                  0.9.2                      py_0    conda-forge
olefile                   0.46                       py_0    conda-forge
openbabel                 3.1.1            py37h311da6c_0    conda-forge
openeye-toolkits          2020.0.4                 py37_0    openeye
openff                    0+untagged.4.g3680de3           dev_0    <develop>
openforcefield            0.7.0+71.g4252f5a7.dirty           dev_0    <develop>
openforcefields           1.2.0                    py37_0    omnia
openmm                    7.4.2           py37_cuda101_rc_1    omnia
openmmforcefields         0.7.2                    py37_0    omnia
openssl                   1.1.1g               h0b31af3_0    conda-forge
packaging                 20.1                       py_0    conda-forge
packmol-memgen            1.1.0rc0                 pypi_0    pypi
pandas                    1.0.3            py37h94625e5_1    conda-forge
pandoc                    2.9.2.1                       0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parmed                    at20RC5+54.g5702a232fe.dirty          pypi_0    pypi
parquet-cpp               1.5.1                         2    conda-forge
parso                     0.7.0              pyh9f0ad1d_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.44                 h4a8c4bd_0    conda-forge
pdb2pqr                   2.1.2+pymol                py_0    schrodinger
pdb4amber                 1.7.dev0                 pypi_0    pypi
perl                      5.26.2            haec8ef5_1006    conda-forge
pexpect                   4.8.0            py37hc8dfbb8_1    conda-forge
pickleshare               0.7.5           py37hc8dfbb8_1001    conda-forge
pillow                    7.1.1            py37hfd78ece_0    conda-forge
pint                      0.11                       py_1    conda-forge
pip                       20.0.2                     py_2    conda-forge
pixman                    0.38.0            h01d97ff_1003    conda-forge
plotly                    4.7.1              pyh9f0ad1d_0    conda-forge
pluggy                    0.12.0                     py_0    conda-forge
pmw                       2.0.1+3                    py_3    schrodinger
prometheus_client         0.7.1                      py_0    conda-forge
prompt-toolkit            3.0.5                      py_0    conda-forge
pthread-stubs             0.4               h1de35cc_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
py                        1.8.1                      py_0    conda-forge
pyarrow                   0.17.1           py37ha1519f6_1    conda-forge
pycairo                   1.19.1           py37h4e38901_3    conda-forge
pycparser                 2.20                       py_0    conda-forge
pydantic                  1.5.1            py37h9bfed18_0    conda-forge
pygments                  2.6.1                      py_0    conda-forge
pymol                     2.3.5            py37h95b93ae_0    schrodinger
pyopenssl                 19.1.0                     py_1    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyqt                      5.9.2            py37h2a560b1_4    conda-forge
pyrsistent                0.16.0           py37h9bfed18_0    conda-forge
pysocks                   1.7.1            py37hc8dfbb8_1    conda-forge
pytest                    5.4.1            py37hc8dfbb8_0    conda-forge
pytest-cov                2.10.0             pyh9f0ad1d_0    conda-forge
python                    3.7.6           h90870a6_5_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.7                     1_cp37m    conda-forge
pytraj                    2.0.5                    pypi_0    pypi
pytz                      2019.3                     py_0    conda-forge
pyyaml                    5.3.1            py37h9bfed18_0    conda-forge
pyzmq                     19.0.0           py37haec44b1_1    conda-forge
qcelemental               0.14.0                     py_0    conda-forge
qcportal                  0.13.1                     py_0    conda-forge
qt                        5.9.7                h8cf7e54_3    conda-forge
rdkit                     2020.03.2        py37h585bbb4_0    conda-forge
re2                       2020.05.01           h4a8c4bd_1    conda-forge
readline                  8.0                  hcfe32e1_0    conda-forge
requests                  2.23.0             pyh8c360ce_2    conda-forge
retrying                  1.3.3                      py_2    conda-forge
rigimol                   1.3                           2    schrodinger
sander                    16.0                     pypi_0    pypi
scikit-learn              0.23.1           py37hf5857e7_0    conda-forge
scipy                     1.4.1            py37hce1b9e5_3    conda-forge
seaborn                   0.10.1                     py_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                46.1.3           py37hc8dfbb8_0    conda-forge
sip                       4.19.8           py37h0a44026_0  
six                       1.14.0                     py_1    conda-forge
smirnoff99frosst          1.1.0                    py37_1    omnia
snappy                    1.1.8                h4a8c4bd_1    conda-forge
snowballstemmer           2.0.0                      py_0    conda-forge
sphinx                    3.1.2                      py_0    conda-forge
sphinx_bootstrap_theme    0.8.0                      py_0    conda-forge
sphinxcontrib-applehelp   1.0.2                      py_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    1.0.3                      py_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.4                      py_0    conda-forge
sqlite                    3.30.1               h93121df_0    conda-forge
statsmodels               0.11.1           py37h9bfed18_1    conda-forge
terminado                 0.8.3            py37hc8dfbb8_1    conda-forge
testpath                  0.4.4                      py_0    conda-forge
threadpoolctl             2.0.0              pyh5ca1d4c_0    conda-forge
thrift-cpp                0.13.0               h0a7acf3_2    conda-forge
tinydb                    4.1.1              pyh9f0ad1d_0    conda-forge
tk                        8.6.10               hbbe82c9_0    conda-forge
toml                      0.10.0                     py_0    conda-forge
tornado                   6.0.4            py37h9bfed18_1    conda-forge
tqdm                      4.46.0             pyh9f0ad1d_0    conda-forge
traitlets                 4.3.3            py37hc8dfbb8_1    conda-forge
urllib3                   1.25.9                     py_0    conda-forge
wcwidth                   0.1.9              pyh9f0ad1d_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.34.2                     py_1    conda-forge
widgetsnbextension        3.5.1                    py37_0    conda-forge
xmltodict                 0.12.0                     py_0    conda-forge
xorg-kbproto              1.0.7             h1de35cc_1002    conda-forge
xorg-libice               1.0.10               h01d97ff_0    conda-forge
xorg-libsm                1.2.3             h01d97ff_1000    conda-forge
xorg-libx11               1.6.9                h0b31af3_0    conda-forge
xorg-libxau               1.0.9                h1de35cc_0    conda-forge
xorg-libxdmcp             1.1.3                h01d97ff_0    conda-forge
xorg-libxext              1.3.4                h01d97ff_0    conda-forge
xorg-libxt                1.2.0                h01d97ff_0    conda-forge
xorg-xextproto            7.3.0             h1de35cc_1002    conda-forge
xorg-xproto               7.0.31            h1de35cc_1007    conda-forge
xz                        5.2.5                h0b31af3_0    conda-forge
yaml                      0.2.4                h0b31af3_0    conda-forge
zeromq                    4.3.2                h6de7cb9_2    conda-forge
zipp                      3.1.0                      py_0    conda-forge
zlib                      1.2.11            h0b31af3_1006    conda-forge
zstd                      1.4.4                h4b3e974_3    conda-forge

Details about conda and system ( conda info ):

(off-dev) jeffreywagner@JW-MBP$ conda info

     active environment : off-dev
    active env location : /Users/jeffreywagner/miniconda3/envs/off-dev
            shell level : 1
       user config file : /Users/jeffreywagner/.condarc
 populated config files : /Users/jeffreywagner/.condarc
          conda version : 4.8.3
    conda-build version : not installed
         python version : 3.8.3.final.0
       virtual packages : __osx=10.14.3
       base environment : /Users/jeffreywagner/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/omnia/osx-64
                          https://conda.anaconda.org/omnia/noarch
                          https://conda.anaconda.org/openeye/osx-64
                          https://conda.anaconda.org/openeye/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/jeffreywagner/miniconda3/pkgs
                          /Users/jeffreywagner/.conda/pkgs
       envs directories : /Users/jeffreywagner/miniconda3/envs
                          /Users/jeffreywagner/.conda/envs
               platform : osx-64
             user-agent : conda/4.8.3 requests/2.24.0 CPython/3.8.3 Darwin/18.2.0 OSX/10.14.3
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Custom build - macOS without FORTRAN?

Note: This is specific to macOS. Linux platforms don't run into this issue, and Windows isn't among our needs here.

Wild idea, but how much of AmberTools depends on compiling FORTRAN code? For context, our OpenFF stack and Psi4 have conflicts that seem to relate to libgfortran, and I'm not sure if the parts of AmberTools we need (primarily antechamber) depend on it. This has me wondering how feasible a stripped-down build would be, one without compiled FORTRAN code, and only for macOS.

This comment provides the most succinct context I can point to: psi4/psi4#2024 (comment)

Ambertools 22 on Python 3.11

Ambertools 23 had a behavior change openmm/openmmforcefields#281 from ambertools 22 that is causing some issues downstream. If we had an ambertools 22 build for python 3.11 (osx-arm arch would be nice as well) then we could keep using ambertools 22 when python 3.10 drops out of NEP.

I am creating this issue to track problems that arise when trying to make a ambertools 22 build for python 3.11. We did try an python 3.11 build for ambertools 22 here #111 but decided to just add a python 3.11 build for ambertools 23.

Missing joblib requirement?

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

We've found that running pip check on packages which install ambertools downstream returns the following: ndfes 1.8 requires joblib, which is not installed..

It looks like there might be some missing joblib dependency in the conda-forge recipe?

Installed packages

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
ambertools                23.0            py310he275f01_0    conda-forge
amberutils                21.0                     pypi_0    pypi
arpack                    3.7.0                hdefa2d7_2    conda-forge
blosc                     1.21.4               h0f2a231_0    conda-forge
boost-cpp                 1.78.0               h6582d0a_3    conda-forge
brotli                    1.0.9                h166bdaf_8    conda-forge
brotli-bin                1.0.9                h166bdaf_8    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.19.1               hd590300_0    conda-forge
ca-certificates           2023.5.7             hbcca054_0    conda-forge
certifi                   2023.5.7           pyhd8ed1ab_0    conda-forge
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7           py310hdf3cbec_0    conda-forge
curl                      8.1.1                h409715c_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.35         py310hc6cd4ac_0    conda-forge
edgembar                  0.2                      pypi_0    pypi
fftw                      3.3.10          nompi_hc118613_107    conda-forge
fonttools                 4.39.4          py310h2372a71_0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
hdf4                      4.2.15               h501b40f_6    conda-forge
hdf5                      1.14.0          nompi_hb72d44e_103    conda-forge
icu                       72.1                 hcb278e6_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4           py310hbf28c38_1    conda-forge
krb5                      1.20.1               h81ceb04_0    conda-forge
lcms2                     2.15                 haa2dc70_1    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.0.6                hcb278e6_1    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_8    conda-forge
libbrotlidec              1.0.9                h166bdaf_8    conda-forge
libbrotlienc              1.0.9                h166bdaf_8    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libcurl                   8.1.1                h409715c_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo             2.1.5.1              h0b41bf4_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libnetcdf                 4.9.2           nompi_h0f3d0bb_105    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libsqlite                 3.42.0               h2797004_0    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtiff                   4.5.0                ha587672_6    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.0                h0b41bf4_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxml2                   2.11.4               h0d562d8_0    conda-forge
libzip                    1.9.2                hc929e4a_1    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
matplotlib-base           3.7.1           py310he60537e_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
netcdf-fortran            4.6.1           nompi_h4f3791c_100    conda-forge
numpy                     1.24.3          py310ha4c1d20_0    conda-forge
openjpeg                  2.5.0                hfec8fc6_2    conda-forge
openssl                   3.1.0                hd590300_3    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h86c2bf4_0    conda-forge
packmol-memgen            2023.2.24                pypi_0    pypi
pandas                    2.0.2           py310h7cbd5c2_0    conda-forge
parmed                    4.1.0           py310heca2aa9_0    conda-forge
pdb4amber                 22.0                     pypi_0    pypi
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pillow                    9.5.0           py310h582fbeb_1    conda-forge
pip                       23.1.2             pyhd8ed1ab_0    conda-forge
platformdirs              3.5.1              pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pymsmt                    22.0                     pypi_0    pypi
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.11         he550d4f_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
sander                    22.0                     pypi_0    pypi
scipy                     1.10.1          py310ha4c1d20_3    conda-forge
setuptools                67.7.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.10               h9fff704_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
typing-extensions         4.6.2                hd8ed1ab_0    conda-forge
typing_extensions         4.6.2              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
unicodedata2              15.0.0          py310h5764c6d_0    conda-forge
urllib3                   2.0.2              pyhd8ed1ab_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.8.4                h8ee46fc_1    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge

Environment info

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     active environment : gufe-clean-testt
    active env location : /home/ialibay/software/mambaforge/install/envs/gufe-clean-testt
            shell level : 1
       user config file : /home/ialibay/.condarc
 populated config files : /home/ialibay/software/mambaforge/install/.condarc
                          /home/ialibay/.condarc
          conda version : 22.9.0
    conda-build version : not installed
         python version : 3.10.8.final.0
       virtual packages : __cuda=12.0=0
                          __linux=5.19.0=0
                          __glibc=2.35=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/ialibay/software/mambaforge/install  (writable)
      conda av data dir : /home/ialibay/software/mambaforge/install/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/ialibay/software/mambaforge/install/pkgs
                          /home/ialibay/.conda/pkgs
       envs directories : /home/ialibay/software/mambaforge/install/envs
                          /home/ialibay/.conda/envs
               platform : linux-64
             user-agent : conda/22.9.0 requests/2.28.1 CPython/3.10.8 Linux/5.19.0-42-generic ubuntu/22.04.2 glibc/2.35
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Procedure for creating updates to AmberTools23?

Comment:

Hi: Pull requests #113 and #116 will require changes to the AmberTools23 source. There seem to be two possible ways to update the conda packages:

1. have ambertools-feedstock access the update.xxx files at ambermd.org, starting from the original (23.0) AmberTools tar file.
2. Create an updated, complete tar file, and have the conda build script pull that.
3. something else??

Option 2 seems easier, but I don't remember doing that in the past. I'm happy to create the updated tar file.

ambertools package vendors packmol

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

AmberTools installs and includes a packmol binary (an old one) which will overwrite the packmol binary installed from the actual packmol package. So you'll see something like the following:

(test-packmol) swails@Batman ~ $ conda list | grep -e ambertools -e packmol
# packages in environment at /scratch2/anaconda3/envs/test-packmol:
ambertools                20.15                    pypi_0    pypi
packmol                   20.2.2               h92ddd45_0    conda-forge
packmol-memgen            1.1.0rc0                 pypi_0    pypi
(test-packmol) swails@Batman ~ $ packmol -v

################################################################################

 PACKMOL - Packing optimization for the automated generation of
 starting configurations for molecular dynamics simulations.
 
                           Included as part of Packmol Memgen
                                                              Version 18.169 

################################################################################

  Packmol must be run with: packmol < inputfile.inp 

  Userguide at: www.ime.unicamp.br/~martinez/packmol 

  Reading input file... (Control-C aborts)
^C

As you can see, conda thinks it installed packmol 20.2.2, but the ambertools package really silently overwrote it with its own copy.

Just like we're switching the ambertools package to depend on parmed (instead of vendoring), we should do the same to packmol, especially if this is going to be an indirect dependency (which it is likely to be given its relationship to openff).

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

Issues related to compiling AmberTools with clang-16

These errors are seen (in old,old,old xleap code):

These are the errors from the osx-64 and osx-arm64

2023-10-06T01:41:17.8020210Z /Users/runner/miniforge3/conda-bld/ambertools_1696552439471/work/AmberTools/src/leap/src/Wc/WcActCB.c:316:5: error: incompatible function pointer types passing 'void (Widget, XtGrabKind)' (aka 'void (struct _WidgetRec *, XtGrabKind)') to parameter of type 'PFVWidInt' (aka 'void (*)(struct _WidgetRec *, int)') [-Wincompatible-function-pointer-types]
2023-10-06T01:41:17.8021260Z                          XtPopup, XtGrabNone );
2023-10-06T01:41:17.8022180Z                          ^~~~~~~

2023-10-06T01:41:17.8025180Z /Users/runner/miniforge3/conda-bld/ambertools_1696552439471/work/AmberTools/src/leap/src/Wc/WcActCB.c:323:5: error: incompatible function pointer types passing 'void (Widget, XtGrabKind)' (aka 'void (struct _WidgetRec *, XtGrabKind)') to parameter of type 'PFVWidInt' (aka 'void (*)(struct _WidgetRec *, int)') [-Wincompatible-function-pointer-types]
2023-10-06T01:41:17.8026070Z                          XtPopup, XtGrabExclusive );
2023-10-06T01:41:17.8026340Z                          ^~~~~~~

2023-10-06T01:41:17.8103750Z /Users/runner/miniforge3/conda-bld/ambertools_1696552439471/work/AmberTools/src/leap/src/Wc/WcActCB.c:916:23: error: incompatible function pointer types passing 'void (Widget, const char *, XtCallbackList)' (aka 'void (struct _WidgetRec *, const char *, struct _XtCallbackRec *)') to parameter of type 'AddOrRemoveProc' (aka 'void (*)(struct _WidgetRec *, char *, struct _XtCallbackRec *)') [-Wincompatible-function-pointer-types]
2023-10-06T01:41:17.8104400Z                                 "WcAddCallbacks", XtAddCallbacks );
2023-10-06T01:41:17.8104690Z                                                   ^~~~~~~~~~~~~~

2023-10-06T01:41:17.8107390Z /Users/runner/miniforge3/conda-bld/ambertools_1696552439471/work/AmberTools/src/leap/src/Wc/WcActCB.c:926:26: error: incompatible function pointer types passing 'void (Widget, const char *, XtCallbackList)' (aka 'void (struct _WidgetRec *, const char *, struct _XtCallbackRec *)') to parameter of type 'AddOrRemoveProc' (aka 'void (*)(struct _WidgetRec *, char *, struct _XtCallbackRec *)') [-Wincompatible-function-pointer-types]
2023-10-06T01:41:17.8107970Z                                 "WcRemoveCallbacks", XtRemoveCallbacks );
2023-10-06T01:41:17.8108230Z                                                      ^~~~~~~~~~~~~~~~~

I don't have access to OSX machines, but have installed clang-16 on my linux (Ubuntu) box, and will see if there is some simple fix. I don't think anyone understands what this code is doing.

Going forward, AmberTools has a significant number of function declataions without prototypes (cpptraj, etc.). These will need to be addressed soon.

AT20 will have a TRUST_SYSTEM_LIBS var we should use

This is just a reminder to set -DTRUST_SYSTEM_LIBS=TRUE when AT20 is released, which will include some of our patches and those will be triggered with that var.