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HTMD: Programming Environment for Molecular Discovery

Home Page: https://software.acellera.com/docs/latest/htmd/index.html

License: Other

Python 10.27% Shell 0.01% Jupyter Notebook 26.87% Batchfile 0.01% Smarty 0.01% Rich Text Format 62.82% Makefile 0.02%

automate drug-discovery htmd molecular-simulations

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htmd's Issues

charmm.search(key='RESI', name = 'CHL1')

I propose this function which should simply grep inside all charmm files to tell me which file provides the RESI CHL1 residue

.wait() method should report if acemd is stuck

Hello,
we are trying to equilibrate the system but when it arrives to "mdx.wait()" it takes too long (more than 2 hours and still running) and in the documentation says it will take 5 minutes.

from htmd.protocols.equilibration_v1 import Equilibration
from natsort import natsorted
md = Equilibration()
md.numsteps = 1000
md.temperature = 298

builds = natsorted(glob('./docked/build/*/'))
for i, b in enumerate(builds):
    md.write(b, 'docked/equil/{}/'.format(i+1))

mdx = AcemdLocal()
mdx.submit(glob('./docked/equil/*/'))

mdx.wait()

It does not give any errors, should we still waiting or is there any errors?

can travis check RH6 as well

Some people have RH6 and sometime there are missing libs.

Parameterization: Could not find binary [g09_wrapper] in PATH

I am using the unpackaged HTMD version with the _readXYZ hotfix (using PYTHONPATH).

Running: parameterize --resume param_at

gives me:

 === Parameterise 2016 ===

      (c) Acellera 
2016-05-25 12:28:25,385 - parameterize - INFO - Resuming job [param_at]
2016-05-25 12:28:25,389 - parameterize - INFO - Could not find binary [g09_wrapper] in PATH 

 Failed to run parameterisation : Prerequisite test failed Could not find binary [g09_wrapper] in PATH

New release for htmd-data necessary [Problem running tests]

I was running tests for #19:

%run tests/run_inline_file_tests.py

And I got this:

Traceback (most recent call last):
  File "./htmd/builder/builder.py", line 341, in <module>
    ref = Molecule(path.join(home(), 'data', 'building-protein-membrane', '1ITG.pdb'))
  File "/home/joao/miniconda3/lib/python3.5/site-packages/htmd/molecule/molecule.py", line 143, in __init__
    self.read(filename)
  File "/home/joao/miniconda3/lib/python3.5/site-packages/htmd/molecule/molecule.py", line 591, in read
    self._readPDB(filename)
  File "/home/joao/miniconda3/lib/python3.5/site-packages/htmd/molecule/molecule.py", line 693, in _readPDB
    raise NameError('File {} not found'.format(filename))
NameError: File /home/joao/miniconda3/lib/python3.5/site-packages/htmd/data/building-protein-membrane/1ITG.pdb not found

In fact, there is no 1ITG.pdb there. Actually, the __name__ of builder.py has this two that won't run the inline file tests:

    mol = Molecule('1ITG')
    ref = Molecule(path.join(home(), 'data', 'building-protein-membrane', '1ITG.pdb'))
    mol = autoSegment(mol, sel='protein')
    assert np.all(mol.segid == ref.segid)

    mol = Molecule('3PTB')
    ref = Molecule(path.join(home(), 'data', 'building-protein-membrane', '3PTB.pdb'))
    mol = autoSegment(mol, sel='protein')
    assert np.all(mol.segid == ref.segid)

Or am I doing something wrong, @stefdoerr?

Minimizing box dimensions

Hi guys,

I know this is a question rather than an issue.

I tried to minimize a huge simulation box. So I did:
a=htmd.builder.builder.minimalRotation(systemCaps)
Where the output was: 1.7853981634 which I thought it is the theta angle for the rotation around Z.
So then I tried:

b=htmd.rotationmatrix.rotationMatrix(z, a)
Traceback (most recent call last):
  File "./scripts/1.build.py", line 26, in <module>
    b=htmd.rotationmatrix.rotationMatrix(z, a)
NameError: name 'z' is not defined

Also triedaxis=z or a number (2, as I thought x could be 0 and y could be 1. Just to try XD)
How do I specify the axis? Besides, is this the correct way to find the matrix for my optimal rotation?

Do you think having an example after each function in the documentation would be worth?

Molecule.rotateBy and Molecule.rotate redundancy

It seems to me that Molecule.rotateBy and Molecule.rotate are redundant.

I was seeing this with @giadefa and it seems like, for example, mol.rotate([0, 1, 0], 1.57) and mol.rotateBy(rotationmatrix([0, 1, 0],1.57)) do the same. So, the key is the rotationmatrix function.

I will still need to see this better, before proposing a change, specially because of the center attribute. And do testing, of course. But, in principle, Molecule.rotateBy could be kept, and Molecule.rotate could be deprecated.

give option to put parameterise files elsewhere than $HOME/.htmd/gaamp

Molecule reading multi-frame PDB

NMR structures for example can have multiple frames

getting pkas for residues

Hello guys,

I am not sure how to use the propka implementation. Following the tutorial I tried:

system = Molecule('4xv1_prep.pdb')
pkas = pka(system , pH=6.5 )
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'pka' is not defined

So then I tried:

from htmd.molecule.pka import pka as pka
>>> pkas = pka(system, pH=6.5 )


During handling of the above exception, another exception occurred:

T
NameError: Failed to execute PropKa

I am using the pfizer version: You are on the latest HTMD version (0.1.32).

Any help is appreciated.

prepareProtein error

Hi all,

I was trying to use proteinPrepare, I think is a nice feature and will be very useful soon.
So first I did:

> >>> protein=Molecule('./model.pdb')
> >>> protein.filter("protein and not resid 1 to 31" )
> >>> protCaps = segmentgaps(protein,'protein','P').
> >>> solvated = solvate(protein)
> >>> detectDisulfideBonds(solvated, minmax=np.vstack((m,M)))
> >>> built= charmm.build(solvated, topo=topos, param=params,outdir='./build')

This builds a system as we could expect. But this doesn't:

>>> protein=Molecule('./model.pdb')
>>> protein.filter("protein and not resid 1 to 31" )
>>> mpp,dat=prepareProtein(protein,returnDetails=True)
Warning: no pdbfile provided
propka3.1                                                                                    2016-04-14
-------------------------------------------------------------------------------------------------------
--                                                                                                   --
--                                   PROPKA: A PROTEIN PKA PREDICTOR                                 --
--                                                                                                   --
--                                 VERSION 1.0,  04/25/2004, IOWA CITY                               --
--                                             BY HUI LI                                             --
--                                                                                                   --
--                            VERSION 2.0,  11/05/2007, IOWA CITY/COPENHAGEN                         --
--                                BY DELPHINE C. BAS AND DAVID M. ROGERS                             --
--                                                                                                   --
--                                VERSION 3.0,  01/06/2011, COPENHAGEN                               --
--                            BY MATS H.M. OLSSON AND CHRESTEN R. SONDERGARD                         --
--                                                                                                   --
--                                VERSION 3.1,  07/01/2011, COPENHAGEN                               --
--                            BY CHRESTEN R. SONDERGARD AND MATS H.M. OLSSON                         --
-------------------------------------------------------------------------------------------------------


-------------------------------------------------------------------------------------------------------
 References:

   Very Fast Empirical Prediction and Rationalization of Protein pKa Values
   Hui Li, Andrew D. Robertson and Jan H. Jensen
   PROTEINS: Structure, Function, and Bioinformatics 61:704-721 (2005)

   Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes
   Delphine C. Bas, David M. Rogers and Jan H. Jensen
   PROTEINS: Structure, Function, and Bioinformatics 73:765-783 (2008)

   PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions
   Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski, and Jan H. Jensen
   Journal of Chemical Theory and Computation, 7(2):525-537 (2011)

   Improved Treatment of Ligands and Coupling Effects in Empirical Calculation
    and Rationalization of pKa Values
   Chresten R. Sondergaard, Mats H.M. Olsson, Michal Rostkowski, and Jan H. Jensen
   Journal of Chemical Theory and Computation, (2011)

-------------------------------------------------------------------------------------------------------



Warning: Missing atoms or failed protonation for C-  331 A (COO) -- please check the structure
         Group (COO) for  4910- OXT   331-LEU (A) [ 124.386    7.622   70.718] O
         Expected 2 interaction atoms for acids, found:
              4910- OXT   331-LEU (A) [ 124.386    7.622   70.718] O
         Expected 2 interaction atoms for bases, found:
              4910- OXT   331-LEU (A) [ 124.386    7.622   70.718] O
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/path/to/htmd/site-packages/htmd/proteinpreparation/proteinpreparation.py", line 141, in prepareProtein
    propkaOptions=propka_opts)
  File "/path/to/htmd/site-packages/htmd/proteinpreparation/pdb2pqr/main.py", line 307, in runPDB2PQR
    pka_molecule, pka_not_found, pkadic = myRoutines.runPROPKA31(propkaOptions)
  File "/path/to/htmd/site-packages/htmd/proteinpreparation/pdb2pqr/src/routines.py", line 1628, in runPROPKA31
    pka_molecule = propka.molecular_container.Molecular_container(HFreeProteinFile.name, pka_options)
  File "/path/to/htmd/site-packages/PROPKA-3.1-py3.5.egg/propka/molecular_container.py", line 54, in __init__
  File "/path/to/htmd/site-packages/PROPKA-3.1-py3.5.egg/propka/molecular_container.py", line 109, in extract_groups
  File "/path/to/htmd/site-packages/PROPKA-3.1-py3.5.egg/propka/conformation_container.py", line 34, in extract_groups
  File "/path/to/htmd/site-packages/PROPKA-3.1-py3.5.egg/propka/group.py", line 1179, in is_group
  File "/path/to/htmd/site-packages/PROPKA-3.1-py3.5.egg/propka/group.py", line 1229, in is_ligand_group_by_groups
  File "/path/to/htmd/site-packages/PROPKA-3.1-py3.5.egg/propka/protonate.py", line 145, in protonate_atom
  File "/path/to/htmd/site-packages/PROPKA-3.1-py3.5.egg/propka/protonate.py", line 170, in set_number_of_protons_to_add
KeyError: ''

Let me know.

Thanks
Noelia

Nice progressbars for Metric

Now that the jupyter guys fixed the bug with joblib not printing parallel jobs I could add a callback to my own progressbar again

Parametrize a .sdf file using htmd

Hello,
Is there any way to parametrize a molecule in .sdf format using htmd? If there is not, is there any way to convert .sdf into .mol2? I guess .mol2 format is the standard one to use in htmd.

Thanks in advance,
Alejandro.

Molecule.append and reordering serials

I have a question: shouldn't Molecule.append reorder the Molecule.serial of the molecule to append to follow the serials of the target molecule?

Example of bug: when appending serials of shorter number than the total number of serials of a protein, they get intercalated between the protein and VMD fails miserably to represent NewCartoon.

Include acemd requirement

TODO

where's data map?

Hi guys,
When projecting with the old method:

data1 = MetricDistance.project(sims, 
    'resname LIG and noh', 
    'resid 88 172 176 180 187 188 189 192 295 296 297 303 304 305 306 308 310 314 317 and name CA',  metric='contacts')

we get some values in data1.map

However if I do the same with the new suggested method:

sims = simlist(glob('filtered/*/'), './filtered/filtered.pdb')
metr=Metric(sims)
metr.projection(MetricDistance('resname LIG and noh', 'resid 88 172 176 180 187 188 189 192 295 296 297 303 304 305 306 308 310 314 317 and name CA', metric='contacts'))
data=metr.project()

data.map is empty.

How can I look what are the indexes after using getStateStatisticnow?

question on dihedral metric usage

Hi guys,

I want use metric dihedral on four specific atoms. I'm using version 1.0.26.
I tried:

sims = simlist(glob('./filtered/*/'), './filtered/filtered.pdb')
metr1=Metric(sims)
sincos=True)) 
metr1.projection(MetricDihedral(dih="index 2629 2625 2623 2608", sincos=True))
data = metr1.project()
NameError: Could not parse selection "i". Is the selection a valid VMD atom selection?

And also tried:

metr1.projection(MetricDihedral(dih=("index 2629", "index 2625", "index 2623", "index 2608"), sincos=True)) 
2016-06-02 14:36:18,184 - htmd.projections.metric - WARNING - Error in simulation with id: 7 index 1 is out of bounds for axis 0 with size 1

This last error happened for all the trajectories.
Any other metrics (contacts, distances) work fine in this system. The selection is valid and correspond to the backbone dihedral of a single aminoacid.

Any ideas?
Thanks,
Noelia

list indices must be integers or slices, not tuple

Hello guys,

Sorry, it seems this function in the documentation might be outdated. Do you perhaps know how can I get the simulation name from data after having used data.dropTraj()?

Thanks a lot,
Noelia

simframes = data.rel2sim([100,56])  
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-84-a4d8c00fd89b> in <module>()
      8 #    if np.any(data.dat[i]<2): print(i,data.dat[i])
      9 #len(sims865)
---> 10 simframes = data.rel2sim([100,56])
     11 #data.plotTrajSizes()
     12 #print(sims865[80])
/path/to/acellera/test/python/lib/python3.5/site-packages/htmd/metricdata.py in rel2sim(self, relFrames)
    369         frames = []
    370         for i in range(np.size(relFrames, 0)):
--> 371             trajID = relFrames[i, 0]
    372             trajFrame = relFrames[i, 1]
    373             sims.append(self.simlist[trajID])
TypeError: list indices must be integers or slices, not tuple

Consider using sparse=True.

Hi guys,

One question. When doing an MSM with lot of data i've come across this warning several times:
2016-05-11 15:07:26,716 - pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM[0] - WARNING - Building a dense MSM with 4956 states. This can be inefficient or unfeasible in terms of both runtime and memory consumption. Consider using sparse=True.

I didn't find where to put the 'sparse=True' flag though. Any ideas?

Thanks,
Noelia

Writing .latestversion on readonly filesystem

By starting HTMD on a readonly installation it has no permission to write latestversion. What is writing?

f = open(fname, 'w')
OSError: [Errno 30] Read-only file system: '/acellera/current/python/lib/python3.5/site-packages/htmd/.latestversion

Support for triple bonds

Hi all,

I was writing this as a parameterization issue but I thought this is rather general.

There's a continuous problem on running simulations with ligands containing triple bonds.
The parameters generated by parameterize crash usually straight away in an ACEMD simulation.
The parameters generated by cgenff aren't unable to run because ACEMD cannot index the topology file for these dihedrals in the parameter file. This is reproducible and occurs with any kind of molecule containing triple bonds. (C-C or C-N)

I have partially found the problem. So basically, dihedrals involving an angle of 180° like in triple bonds are mathematically undefined. As such, CHARMM does not require them to be present in the MD software, and the CGenFF program doesn't generate them accordingly. ACEMD or NAMD need all the topology atoms to be indexed in the parameter file, and then we always miss the dihedral of the triple bond, so the simulation doesnt run. The same applies to parameterize, as it relies on cgennff in first place.

The solution is basically writing manually the dihedral as the charmm MD engine would read it. Given the dihedral formula used in charmm:

V(dihedral) = Kchi(1 + cos(n(chi) - delta))
We need to put an amplitude Kchi = 0, multiplicity of n= 2 and delta = 180 degrees.

We might need to include an automatic way to parse triple bonds which are missing and write out this dihedral automatically.

Thanks,
Noelia

reporting tool

Hi guys,

Just to know, I haven't heard about it for a while, are you still using the adaptive reporting tool (back in matlab times function called reportProtLig) ?
If so, is it implemented in htmd?

Thanks

charmm.built WARNING - Failed/poorly guessed coordinates can cause simulations to crash since failed atoms are all positioned on (0,0,0).

This is kind of wrong, because it is saying that even when there are no [0,0,0] coordinates.
On the other hands it should be make it very clear that it is likely wrong to have it. Like SEVERE WARNING

Bootstrapping tutorial

Hi guys,

I was wondering what would you think about having a bootstrapping tutorial showing the importance of having solid and statistically significant results?

Thanks,
Noelia

proteinpreparation is not currently working

It's returning the protein unmodified. Fixes in progress.

Tutorials: Getting started with HTMD, Playing with HTMD Molecules and Atom Selections

I am going through the tutorials and fixing them.

I think that the "Getting started with HTMD" tutorial [1] and the "Playing with HTMD Molecules" tutorial [2] strongly overlap and could be condensed into only one tutorial called "Getting started with HTMD Molecules", where the Molecule class and its features are introduced.

Furthermore, the "Atom selections" tutorial [3], where @tonigi did an awesome job, is actually more like a documentation page rather than a tutorial. My idea would be to use this material intercalated with snippets of code to take advantage of the notebook capabilities. @giadefa told me this was created as a presentation, but I don't it will lose its purpose as that.

Task list:

~~get rid of redundancies in the first two tutorials~~
~~create a new tutorial which is a fusion of tutorials [1] and [2]~~
~~incorporate the tutorial [3] into the new tutorial, making an extended and dedicated overview of the Molecule class, selection capabilities, features and methods~~ (postponed)

Segmentation Fault in 'Parameterise' doing the Tutorial

Hi,

I followed the last htmd workshop via streaming and I was amazed by the work done by MJ Harvey with GAAMP in Parameterise. Yesterday I wanted to check if it is a tool we have to try in the lab and I found the following:

anaconda2/envs/mylab3/bin/htmd_babel

After installing htmd with conda I had to change the bin/htmd_babel script to:

DIR="path_to/anaconda2/pkgs/htmdbabel-2.3.93-py35_0"; BABEL_DATADIR="$DIR/share/openbabel" "$DIR/bin/htmd_babel.bin" $@

parameterise/share/scripts/nonpolar/000-input

There is a typo in the openbabel output format -o xyz producing the error:

Failed to run parameterisation : run(): Step [input] did not produce the expected output: ['ligand.xyz'] in directory /home/diego/.htmd/gaamp/ethanol/000-input

htmd_babel.bin

The openbabel executable compiled in the htmd conda package gives the following message:

==============================
*** Open Babel Error  in RegisterOptionParam
  The number of parameters needed by option "r" in Point cloud on VDW surface differs from an earlier registration.
==============================
*** Open Babel Error  in RegisterOptionParam
  The number of parameters needed by option "x" in Point cloud on VDW surface differs from an earlier registration.
==============================
*** Open Babel Error  in RegisterOptionParam
  The number of parameters needed by option "s" in VDW surface in binary STL format suitable for 3D printing differs from an earlier registration.
==============================
*** Open Babel Error  in RegisterOptionParam
  The number of parameters needed by option "c" in VDW surface in binary STL format suitable for 3D printing differs from an earlier registration.
1 molecule converted
4 errors 9 info messages 6 audit log messages

These errors disappear in this first step (000-input) when Parameterisation is invoked calling to my local babel. Is there any reason not to include openbabel as a dependency?

parameterise/share/scripts/nonpolar/scripts

The command source ../routines is not recognized by /bin/sh in those distributions where this is a symbolic link to /bin/dash. The header of the scripts were replaced with #!/bin/bash.

Segmentation Fault with parameterise/share/bin/equiv_atom

The tutorial stops in the step 030-generate_structure with:

../routines: line 42: 21467 Segmentation fault      (core dumped) $@ > .$b.txt

Commenting the lines regarding equiv_atom produces a similar error this time with binary add_tip3.

What am I doing wrong?

Hello world!

reconstructAdaptiveTraj TypeError: object of type 'Sim' has no len()

Hello guys,

Not sure what I'm doing wrong.

Thanks,
Noelia

mol, chain, pathlist = reconstructAdaptiveTraj(sims, 55)

/path/to/acellera/test/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.flux' detected! Please use 'msmtools.flux' in the future.
  category=PyEMMA_DeprecationWarning)
/path/to/acellera/test/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.generation' detected! Please use 'msmtools.generation' in the future.
  category=PyEMMA_DeprecationWarning)
/path/to/acellera/test/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.analysis' detected! Please use 'msmtools.analysis' in the future.
  category=PyEMMA_DeprecationWarning)
/path/to/acellera/test/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.dtraj' detected! Please use 'msmtools.dtraj' in the future.
  category=PyEMMA_DeprecationWarning)
/path/to/acellera/test/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.estimation' detected! Please use 'msmtools.estimation' in the future.
  category=PyEMMA_DeprecationWarning)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-29-a90feffab4cf> in <module>()
      1 #len(sims)
----> 2 mol, chain, pathlist = reconstructAdaptiveTraj(sims, 55)

/path/to/acellera/test/python/lib/python3.5/site-packages/htmd/adaptive/adaptive.py in reconstructAdaptiveTraj(simlist, trajID)
    418     for i, c in enumerate(chain):
    419         tmpmol = Molecule(sim.molfile)
--> 420         tmpmol.read(c[0])
    421         endpiece = c[1]
    422         fileloc = np.vstack(tmpmol.fileloc)

/path/to/acellera/test/python/lib/python3.5/site-packages/htmd/molecule/molecule.py in read(self, filename, type, skip, frames, append)
    634             firstfile = filename[0]
    635         else:
--> 636             if len(filename) != 4 and not os.path.exists(filename):
    637                 raise FileNotFoundError('File {} was not found.'.format(filename))
    638             firstfile = filename

TypeError: object of type 'Sim' has no len()

FileNotFoundError: Could not find libs.

Hi guys,

I'm in version 1.0.26. I run: model.viewStates(ligand="resname MOL and noh"). And got the following error:
What am I missing?

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.dtraj' detected! Please use 'msmtools.dtraj' in the future.
  category=PyEMMA_DeprecationWarning)
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.analysis' detected! Please use 'msmtools.analysis' in the future.
  category=PyEMMA_DeprecationWarning)
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.generation' detected! Please use 'msmtools.generation' in the future.
  category=PyEMMA_DeprecationWarning)
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.flux' detected! Please use 'msmtools.flux' in the future.
  category=PyEMMA_DeprecationWarning)
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.estimation' detected! Please use 'msmtools.estimation' in the future.
  category=PyEMMA_DeprecationWarning)

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-5-119f81c50177> in <module>()
      2 #model.load('model-oldsimdata_25+.dat')
      3 os.chdir('/hpc/grid/wip_cmg_wwmc/workspace/groups/neuro_cc/acellera/tmp/proteins/D3R/batches')
----> 4 model.viewStates(ligand="resname MOL and noh")

/path/to/htmd/model.py in viewStates(self, states, statetype, protein, ligand, viewer, mols, numsamples, wrapsel, alignsel)
    395             states = [states]
    396         if mols is None:
--> 397             mols = self.getStates(states, statetype, numsamples=numsamples, wrapsel=wrapsel, alignsel=alignsel)
    398         colors = [0, 1, 3, 4, 5, 6, 7, 9]
    399         for i, s in enumerate(states):

/path/to/htmd/model.py in getStates(self, states, statetype, wrapsel, alignsel, alignmol, samplemode, numsamples)
    346         # Removed ncpus because it was giving errors on some systems.
    347         mols = Parallel(n_jobs=1, verbose=11)(delayed(_loadMols)(self, i, rel, molfile, wrapsel, alignsel, refmol)
--> 348                                                   for i, rel in enumerate(relframes))
    349         return np.array(mols, dtype=object)
    350 

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in __call__(self, iterable)
    798             # was dispatched. In particular this covers the edge
    799             # case of Parallel used with an exhausted iterator.
--> 800             while self.dispatch_one_batch(iterator):
    801                 self._iterating = True
    802             else:

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in dispatch_one_batch(self, iterator)
    656                 return False
    657             else:
--> 658                 self._dispatch(tasks)
    659                 return True
    660 

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in _dispatch(self, batch)
    564 
    565         if self._pool is None:
--> 566             job = ImmediateComputeBatch(batch)
    567             self._jobs.append(job)
    568             self.n_dispatched_batches += 1

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in __init__(self, batch)
    178         # Don't delay the application, to avoid keeping the input
    179         # arguments in memory
--> 180         self.results = batch()
    181 
    182     def get(self):

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in __call__(self)
     70 
     71     def __call__(self):
---> 72         return [func(*args, **kwargs) for func, args, kwargs in self.items]
     73 
     74     def __len__(self):

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in <listcomp>(.0)
     70 
     71     def __call__(self):
---> 72         return [func(*args, **kwargs) for func, args, kwargs in self.items]
     73 
     74     def __len__(self):

/path/to/htmd/model.py in _loadMols(self, i, rel, molfile, wrapsel, alignsel, refmol)
    522         trajs = np.append(trajs, f.sim.trajectory[f.piece])
    523         frs = np.append(frs, f.frame)
--> 524     mol.read(trajs, frames=frs)
    525     if len(wrapsel) > 0:
    526         mol.wrap(wrapsel)

/path/to/htmd/molecule/molecule.py in read(self, filename, type, skip, frames, append)
    670             self._readPDB(filename, mode='pdbqt')
    671         elif (type is None and firstfile.endswith(".xtc")) or type == "xtc":
--> 672             self._readTraj(filename, skip=skip, frames=frames, append=append)
    673         elif (type is None and firstfile.endswith(".coor")) or type == "coor":
    674             self._readBinCoordinates(filename)

/path/to/htmd/molecule/molecule.py in _readTraj(self, filename, skip, frames, append, mdtraj)
    914                     traj.coords = traj.coords[:, :, frames[i]]
    915                 else:
--> 916                     traj = XTCread(f, frames[i])
    917                 self.fileloc.append([f, int(frames[i])])
    918 

/path/to/htmd/molecule/xtc.py in XTCread(filename, frames)
     52 
     53 def XTCread(filename, frames=None):
---> 54     lib = xtc_lib()
     55     nframes = pack_ulong_buffer([0])
     56     natoms = pack_int_buffer([0])

/path/to/htmd/molecule/xtc.py in xtc_lib()
     35 def xtc_lib():
     36     lib = {}
---> 37     libdir = htmd.home(libDir=True)
     38 
     39     import platform

/path/to/htmd/home.py in home(dataDir, libDir)
     45             return os.path.join(libdir, "pro", platform.system())
     46         else:
---> 47             raise FileNotFoundError('Could not find libs.')
     48     else:
     49         return homeDir

FileNotFoundError: Could not find libs.

repulsionconstant, repulsionrange, repulsionadd in ACEMD.

Hello,

Are these functions still available in acemd? I get the following error when I try to use any or them:

#WARNING: cannot open file "restart.coor"
#     Step        Bond       Angle       Dihed        Elec         VDW          PE          KE    External       Total        Temp        Pres     PresAve
         0   6154.7087  23437.9278  17360.4020  -190868.8324     2286.8527  -141628.9413    48289.0165      0.0000  -93339.9248   302.4192      0.0000      0.0000
9.0
TCL error at line #1 []
ERROR: file deven.cpp line 807: TCL evaluation of [calcforces_init]

PS: I'm trying to set a potential among neutral ligands in a membrane. It would be ideal to have only one ligand per box but that's of course too consuming. If you come up with a better idea of setting a potential among them it'd highly appreciate it!

Noelia

Proposal of a 'quality check function' before building

Hi guys,

I was checking how htmd supports ions in charmm or amber. In the figure below you can see the ions with occurrences in the PDB database (just to have a reference), the available ions in charmm and amber and their resnames.
So building a system with a pdb containing K crashes in charmm if not previously renamed to POT. Of course it's up to the users to correctly name the residues in their systems, but what I'm suggesting is that perhaps it doesnt take too long to include a quality check in charmm and amber.build; like if there's present a resname K in the Molecule, rename it automatically to POT. Would this work? The good thing is that in Amber most of the residue names are the same as in the pdb.

Of course it's only a suggestion but it could be a nice feature.
Noelia

Tutorials: optimization and reorganization

Incorporate the missing fixes from my old branch j3mdamas/htmd
Organize the current tutorials.

For each tutorial:

Fix any outdated part
Rename the tutorial to make more sense (people may not know that benzamidin-trypsin is a protein-ligand system, so they need to be more obvious in the navigation bar)
Transform it into presentation if not in it already

Python Primer
Introduction to Atom Selections
Getting Started with HTMD Molecules
System Building Basics
System Building Protein-Ligand
System Building Protein in Membrane
System Building Protein-Protein

amber capping

Hi guys,

I was given this protein [attached] which I have to run in Amber.:

protein=Molecule('protein.pdb')
protein.filter('protein and noh')
protCaps = autoSegment(protein,'protein','P')
protCaps.center()
D = maxDistance(protCaps, 'all') 
solvated = solvate(protCaps,minmax=[[-D, -D, -D], [D, D, D]])
ffs = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
molbuilt = amber.build(solvated, ff=ffs, outdir='.', saltconc=0.15)

I try to build it and get this error:

Videos from the HTMD2015 workshops are available on the Acellera youtube channel: https://www.youtube.com/user/acelleralive

You are on the latest HTMD version (1.0.16).
Solvating: 100% (1/1) [#########################################################################################################################################################################################################] eta --:-- -
Traceback (most recent call last):
  File "./1.build.py", line 36, in <module>
    molbuilt = amber.build(solvated, ff=ffs, outdir='.', saltconc=0.15)
  File "/path/to/htmd/lib/python3.5/site-packages/htmd/builder/amber.py", line 109, in build
    _applyCaps(mol, caps)
  File "/path/to/htmd/lib/python3.5/site-packages/htmd/builder/amber.py", line 216, in _applyCaps
    raise AssertionError('Segment {}, resid {} should have either one H2 or one HT2 atom. Cannot cap.'.format(seg, np.min(resids)))
AssertionError: Segment P, resid 1 should have either one H2 or one HT2 atom. Cannot cap.

So I was wondering what are the conditions of a correct protein to be capped?

protein.txt

Total association free energy

People want to know the total free energy of association, not per-state, since some experiments measure that.

Patches and cofactors in charmm

Hello guys,

I am not finding an easy way to add patches or parameterize cofactors whose parameters are included in charmm already (like phosphates (TP2), hemoglobine (HEME), INO1.. etc)

The problem comes from the fact that these RESIs are (only) included in the charmm_27prot_na ff. This has two consequences:

(probably) many of the most standard patches and cofactors haven't been reparameterized since the release of C27.
Adding patches using the lastest ff requieres sourcing the ff of the patch (RESI), which also depends on the charmm27na ff atomtypes. You can of course separate the RESI you want to apply along with the atomtypes it depends on (select those manually, and are different depending on the residue) in a separate file.

I was wondering if this workaround in 2), which is error-prone and requires a lot of manual intervention could be easily handled with htmd. Phosphates, hemoglobines and other molecules are present in everyday simulations.
The other question is if these RESIs wouldnt be better described with parameterise.

Let me know what you think.

Using docking tool

Hi there,

I am having problems when trying to use the docking tool. I follow the steps for the example on the tutorial (https://www.htmd.org/docs/tutorials/docking-simulation-generators.html), but I receive the following error:

In [1]: from htmd import *
Videos from the HTMD2015 workshops are available on the Acellera youtube channel: https://www.youtube.com/user/acelleralive

You are on the latest HTMD version (1.0.16).

In [2]: htmd.config(viewer='ngl')

In [3]: prot = Molecule('bentryp/trypsin.pdb')

In [4]: prot.center()

In [5]: lig = Molecule('bentryp/benzamidine.pdb')

In [6]: poses, scores = dock(prot, lig)

TypeError Traceback (most recent call last)
in ()
----> 1 poses, scores = dock(prot, lig)

/Users/asr2031/miniconda3/lib/python3.5/site-packages/htmd/dock.py in dock(protein, ligand, center, extent)
97 #from IPython.core.debugger import Tracer
98 #Tracer()()
---> 99 call([babelexe, '-i', 'pdb', protein_pdb, '-o', 'pdbqt', protein_pdbqt, '-xr'])
100 call([babelexe, '-i', 'pdb', ligand_pdb, '-o', 'pdbqt', ligand_pdbqt, '-xhn'])
101

/Users/asr2031/miniconda3/lib/python3.5/subprocess.py in call(timeout, _popenargs, *_kwargs)
558 retcode = call(["ls", "-l"])
559 """
--> 560 with Popen(_popenargs, *_kwargs) as p:
561 try:
562 return p.wait(timeout=timeout)

/Users/asr2031/miniconda3/lib/python3.5/subprocess.py in init(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds)
948 c2pread, c2pwrite,
949 errread, errwrite,
--> 950 restore_signals, start_new_session)
951 except:
952 # Cleanup if the child failed starting.

/Users/asr2031/miniconda3/lib/python3.5/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
1465 else:
1466 env_list = None # Use execv instead of execve.
-> 1467 executable = os.fsencode(executable)
1468 if os.path.dirname(executable):
1469 executable_list = (executable,)

/Users/asr2031/miniconda3/lib/python3.5/os.py in fsencode(filename)
818 return filename.encode(encoding, errors)
819 else:
--> 820 raise TypeError("expect bytes or str, not %s" % type(filename).name)
821
822 def fsdecode(filename):

TypeError: expect bytes or str, not NoneType

In [7]:

I appreciate the help.

Asghar

Could Not Type Atom C10 With State C.3%4A

I'm moving the parameterization issues here as you told me.
Just got the following error, I can send the ligand by email. The initial mol2 file has the sybyl atomtype format, not sure if it matters.

You are on the latest HTMD version (1.0.26).

 === Parameterise 2016 ===

      (c) Acellera 
        AsymmetricTorsion False
                    Debug False
                   E14FAC 1.0
               Equivalent None
            ExecutionMode LSF
                 FileName mol.mol2
               FixCharges None
             GAUSS_SCRDIR /tmp
                  JobName XXXX04965842
                   MEMORY 8
               MaxTorsion 25
                    Model Nonpolar
             Multiplicity 1
                   NCORES 4
                NetCharge 0
                  Neutral None
                 Torsions []
       w_H_Donor_Acceptor 1.0
                  w_alpha 0.4
                 w_charge 3.0
                  w_thole 0.2
            w_water_E_min 0.4
            w_water_R_min 8.0
                 wd_alpha 0.4
                wd_charge 1.0
                 wd_thole 0.2
           wd_water_E_min 0.4
           wd_water_R_min 8.0

Running step [000] [input]
2016-06-03 16:50:12,199 - parameterise.step - INFO - run(): Step [preoptimize] in dir [/home/ferrun/.htmd/gaamp/XXXX04965842/010-preoptimize]
2016-06-03 16:50:12,201 - parameterise.step - INFO - completed(): Expected outputfile [mol-opt.xyz] not present
2016-06-03 16:50:12,205 - parameterise.step - INFO - run(): Running step [preoptimize]
2016-06-03 16:50:12,205 - parameterise.step - INFO -  Running step [10]     [preoptimize] 
Running step [010] [preoptimize]
2016-06-03 16:52:27,709 - parameterise.step - INFO - run(): Step [initial_parameters] in dir [/home/ferrun/.htmd/gaamp/XXXX04965842/020-initial_parameters]
2016-06-03 16:52:27,714 - parameterise.step - INFO - completed(): Expected outputfile [mol.rtf] not present
2016-06-03 16:52:27,719 - parameterise.step - INFO - run(): Running step [initial_parameters]
2016-06-03 16:52:27,720 - parameterise.step - INFO -  Running step [20]     [initial_parameters] 

Running step [020] [initial_parameters]

 Failed to run parameterisation : 
 Failure in step   : initial_parameters
   Directory       : /home/ferrun/.htmd/gaamp/XXXX04965842/020-initial_parameters
   Return value    : 1
   Output          : 
 -- 
==============================
*** Open Babel Error  in RegisterOptionParam
  The number of parameters needed by option "r" in Point cloud on VDW surface differs from an earlier registration.
==============================
*** Open Babel Error  in RegisterOptionParam
  The number of parameters needed by option "x" in Point cloud on VDW surface differs from an earlier registration.
==============================
*** Open Babel Error  in RegisterOptionParam
  The number of parameters needed by option "s" in VDW surface in binary STL format suitable for 3D printing differs from an earlier registration.
==============================
*** Open Babel Error  in RegisterOptionParam
  The number of parameters needed by option "c" in VDW surface in binary STL format suitable for 3D printing differs from an earlier registration.
==============================
*** Open Babel Warning  in Init
  Cannot open element.txt defaulting to compiled data.
==============================
*** Open Babel Warning  in Init
  Cannot open bondtyp.txt defaulting to compiled data.
==============================
*** Open Babel Warning  in Init
  Cannot open aromatic.txt defaulting to compiled data.
==============================
*** Open Babel Warning  in Init
  Cannot open atomtyp.txt defaulting to compiled data.
1 molecule converted
4 errors 4 warnings 18 audit log messages 
Could Not Type Atom C10 With State C.3%4A at /path/to/acellera/current/python/lib/python3.5/site-packages/parameterise/share/match/bin/../MATCH//lib/MATCHer.pm line 158

Trajectory view with NGL viewer does not show anything

Reproducer

molTraj = Molecule(htmd.home() + '/data/dhfr/dhfr.psf')
molTraj.read(htmd.home() + '/data/dhfr/dhfr.xtc')
molTraj.view()

model has not been estimated

Hi guys,

I have come across an error when plotting timescales a few times now, but I don't know what I'm doing wrong.
The error is huge, it's attached. Apparently the last line read:

AttributeError: Model has not yet been estimated. Call estimate(X) or fit(X) first

I have however run many times model=model(dataTica). But it doesn't seem to be the reason.
Any help appreciated!

Noelia

error_impliedtimescales.txt

Broader metrictypes in adaptive

Not really an issue, but I was wondering if it would be interesting to have different metrics other than contacts and distances during the adaptive.

Besides, what happened to a secondary-structure driven adaptive that I recall from the past? Did that work? @stefdoerr (Did that exist?)

Parameterize tutorial

benzamidine

markovModel(lag,n + 1)

Hello!

Question. It seems that sometimes lately when I try to build n macrostates I get n-1, is this an error?

Thanks,
Noelia

model=Model(dataTica)
#model.plotTimescales(lags=range(1,100,5))
model.markovModel(50,5)
model.viewStates(protein="protein and name CA")

2016-06-07 12:58:55,952 - htmd.model - INFO - 24.4% of the data was used
2016-06-07 12:58:55,959 - htmd.model - INFO - Number of trajectories that visited each macrostate:
2016-06-07 12:58:55,960 - htmd.model - INFO - [5 4 5 2]
2016-06-07 12:58:55,962 - htmd.model - INFO - Take care! Macro 3 has been visited only in 2 trajectories:
2016-06-07 12:58:55,962 - htmd.model - INFO - id = 15
parent = None
input = []
trajectory = ['./filtered/e2s6_e1s8p0f473/output.filtered.xtc']
molfile = ./filtered/filtered.pdb
2016-06-07 12:58:55,963 - htmd.model - INFO - id = 16
parent = None
input = []
trajectory = ['./filtered/e2s7_e1s8p0f331/output.filtered.xtc']
molfile = ./filtered/filtered.pdb
[Parallel(n_jobs=1)]: Done   1 tasks       | elapsed:    6.8s
[Parallel(n_jobs=1)]: Done   2 tasks       | elapsed:   13.9s
[Parallel(n_jobs=1)]: Done   3 tasks       | elapsed:   20.5s
[Parallel(n_jobs=1)]: Done   4 tasks       | elapsed:   27.2s
[Parallel(n_jobs=1)]: Done   4 out of   4 | elapsed:   27.2s finished

VdW table too large ERROR

Hi guys,

I have a system with two ligands. 1 of them parameterized with cgenff latest version through command line the other with parameterize. It's basically running a simulation of pdb file 4MQT.
I run this system with both par/par_all36_prot.prm and par/par_all36_prot_mod.prm.
It turns that the first works straight away the second cannot find atomtype xxxx. which is found in the cgenff ligand.

Let me know if you need all the files.

best
N

Parametrise: run(): Step [input] did not produce the expected output

Hi,
I wanted to try parameterise, so I installed it and set up a simple test system, but when I trie to run it (from command line or within a python script) it dies with the error in the title.
Here's what I did:

installed through

conda install parametrise -c acellera

the molecule file (3mpr_ac.mol2) and the input file (pjob) are attached below.
pjob contains this:

JobName 3mpr_test
FileName 3mpr_ac.mol2
NetCharge 0

calling parameterise this way

parameterise --input pjob

returns this:

Videos from the HTMD2015 workshops are available on the Acellera youtube channel: https://www.youtube.com/user/acelleralive

You are on the latest HTMD version (1.0.8).

 === Parameterise 2016 ===

      (c) Acellera 
        AsymmetricTorsion False
                    Debug False
                   E14FAC 1.0
               Equivalent None
            ExecutionMode Inline
                 FileName 3mpr_ac.mol2
               FixCharges None
             GAUSS_SCRDIR /tmp
                  JobName 3mpr_test
                   MEMORY 8
               MaxTorsion 25
                    Model Nonpolar
             Multiplicity 1
                   NCORES 8
                NetCharge 0
                  Neutral None
                 Torsions []
       w_H_Donor_Acceptor 1.0
                  w_alpha 0.4
                 w_charge 3.0
                  w_thole 0.2
            w_water_E_min 0.4
            w_water_R_min 8.0
                 wd_alpha 0.4
                wd_charge 1.0
                 wd_thole 0.2
           wd_water_E_min 0.4
           wd_water_R_min 8.0

Running step [000] [input]

 Failed to run parameterisation : run(): Step [input] did not produce the expected output: ['ligand.xyz'] in directory /home/ggutierrez/.htmd/gaamp/3mpr_test/000-input

additional note: gaussian is correctly installed in its version 09 with all the necessary environment variables set up, but the value of GAUSS_SCRDIR in this output doesn't match the one i configured.
( /tmp vs /data3/g09scr )

am I missing something here?

files.zip

Amber aliasing

Hi guys,

One question. Is amber.build aliasing residues in the same way as charmm.build does?
I just built a system in charmm whose initial receptor structure contained a terminal patch called 'NMA' (not appearing in the final structure.pdb). However the same system didnt work in amber.build giving the following error:
FATAL: Atom .R< NMA 466 >.A<N 1> does not have a type

But I remember charmm was also having this issue some weeks ago, so I guess charmm.build is now automatically removing terminal patches from the initial structure. Is this correct?

Thanks,
Noelia

caps in amber

Hi all,

Got this error when building an amber system. It's a bit strange because I think this same system worked a couple of weeks ago and also works in charmm. The protein I'm using is 5hd0.pdb and saving chain A (attached solvated molecule a txt file, pdbs aren't supported here).

solvated.txt

raise AssertionError('Segment {}, resid {} should have either one H2 or one HT2 atom. Cannot cap.'.format(seg, np.min(resids)))

AssertionError: Segment P0, resid 58 should have either one H2 or one HT2 atom. Cannot cap.

Thanks

Create a tutorial for the Metric class and the projections workflow

guess bond error in filter

OSX

2016-06-06 22:37:39,866 - htmd.molecule.molecule - INFO - Attempting PDB query for 2OV5

ValueError Traceback (most recent call last)
in ()
1 m = Molecule('2OV5')
----> 2 m.filter('protein or water')

/Users/gianni/miniconda3/lib/python3.4/site-packages/htmd/molecule/molecule.py in filter(self, sel, _logger)
491 >>> mol.filter('protein')
492 '''
--> 493 s = self.atomselect(sel)
494 if np.all(s): # If all are selected do nothing
495 return

/Users/gianni/miniconda3/lib/python3.4/site-packages/htmd/molecule/molecule.py in atomselect(self, sel, indexes, strict, fileBonds, guessBonds)
457 chain=self.chain,
458 segname=self.segid, insert=self.insertion, altloc=self.altloc, beta=self.beta,
--> 459 occupancy=self.occupancy, bonds=self._getBonds(fileBonds, guessBonds))
460 if np.sum(s) == 0 and strict:
461 raise NameError('No atoms were selected with atom selection "{}".'.format(sel))

/Users/gianni/miniconda3/lib/python3.4/site-packages/htmd/molecule/molecule.py in _getBonds(self, fileBonds, guessBonds)
420 bonds = numpy.vstack((bonds, self.bonds))
421 if guessBonds:
--> 422 bonds = numpy.vstack((bonds, self._guessBonds()))
423 return bonds
424

/Users/gianni/miniconda3/lib/python3.4/site-packages/htmd/molecule/molecule.py in _guessBonds(self)
526 framecoords = self.coords[:, :, self.frame].copy()
527 return guessbonds(framecoords, self.element, self.name, self.resname, self.resid, self.chain, self.segid,
--> 528 self.insertion, self.altloc)
529
530 def moveBy(self, vector, sel=None):

/Users/gianni/miniconda3/lib/python3.4/site-packages/htmd/molecule/vmdparser.py in guessbonds(coordinates, atomname, atomtype, resname, resid, chain, segname, insertion, altloc)
236
237 if(retval):
--> 238 raise ValueError("Guessed bonding is bad")
239 #print(retval)
240 nbonds = c_nbonds[0]

ValueError: Guessed bonding is bad

Parameterize Non-zero exit code from [..]/equiv_atom:

10/23 ligands exited today with this error, whats also the warning?

Thanks.

2016-06-03 08:40:28,386 - gaamp - INFO - Staging in input mol2/pdb file
2016-06-03 08:40:28,500 - parameterise.step - INFO - run(): Starting run in [/home/ferrun/.htmd/gaamp/2vt4]
2016-06-03 08:40:28,500 - parameterise.step - INFO - run(): Step [input] in dir [/home/ferrun/.htmd/gaamp/2vt4/000-input]
2016-06-03 08:40:28,501 - parameterise.step - INFO - completed(): Expected outputfile [ligand.xyz] not present
2016-06-03 08:40:28,501 - parameterise.step - INFO - run(): Running step [input]
2016-06-03 08:40:28,501 - parameterise.step - INFO -  Running step [0]  [input] 
Please cite. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery, J. Chem. Theory Comput., 2016, 12 (4), pp 1845-1852. http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00049


You are on the latest HTMD version (1.0.26).

 === Parameterise 2016 ===

      (c) Acellera 
        AsymmetricTorsion False
                    Debug False
                   E14FAC 1.0
               Equivalent None
            ExecutionMode LSF
                 FileName mol.mol2
               FixCharges None
             GAUSS_SCRDIR /tmp
                  JobName 2vt4
                   MEMORY 8
               MaxTorsion 25
                    Model Nonpolar
             Multiplicity 1
                   NCORES 4
                NetCharge 1
                  Neutral None
                 Torsions []
       w_H_Donor_Acceptor 1.0
                  w_alpha 0.4
                 w_charge 3.0
                  w_thole 0.2
            w_water_E_min 0.4
            w_water_R_min 8.0
                 wd_alpha 0.4
                wd_charge 1.0
                 wd_thole 0.2
           wd_water_E_min 0.4
           wd_water_R_min 8.0

Running step [000] [input]
2016-06-03 08:40:28,890 - parameterise.step - INFO - run(): Step [preoptimize] in dir [/home/ferrun/.htmd/gaamp/2vt4/010-preoptimize]
2016-06-03 08:40:28,892 - parameterise.step - INFO - completed(): Expected outputfile [mol-opt.xyz] not present
2016-06-03 08:40:28,895 - parameterise.step - INFO - run(): Running step [preoptimize]
2016-06-03 08:40:28,895 - parameterise.step - INFO -  Running step [10]     [preoptimize] 
Running step [010] [preoptimize]
2016-06-03 08:41:44,301 - parameterise.step - INFO - run(): Step [initial_parameters] in dir [/home/ferrun/.htmd/gaamp/2vt4/020-initial_parameters]
2016-06-03 08:41:44,304 - parameterise.step - INFO - completed(): Expected outputfile [mol.rtf] not present
2016-06-03 08:41:44,306 - parameterise.step - INFO - run(): Running step [initial_parameters]
2016-06-03 08:41:44,307 - parameterise.step - INFO -  Running step [20]     [initial_parameters] 

Running step [020] [initial_parameters]
2016-06-03 08:41:51,811 - parameterise.step - INFO - run(): Step [generate_structure] in dir [/home/ferrun/.htmd/gaamp/2vt4/030-generate_structure]
2016-06-03 08:41:51,813 - parameterise.step - INFO - completed(): Expected outputfile [mol.xpsf] not present
2016-06-03 08:41:51,829 - parameterise.step - INFO - run(): Running step [generate_structure]
2016-06-03 08:41:51,830 - parameterise.step - INFO -  Running step [30]     [generate_structure] 
Running step [030] [generate_structure]

 Failed to run parameterisation : 
 Failure in step   : generate_structure
   Directory       : /home/ferrun/.htmd/gaamp/2vt4/030-generate_structure
   Return value    : 1
   Output          : 
 -- 
# WARNING. This build is about to expire. Please write to [email protected] for more information.
# WARNING. This build has expired. Please write to [email protected] for more information.
Non-zero exit code from /path/to/acellera/current/python/lib/python3.5/site-packages/parameterise/share/bin/equiv_atom: 
# WARNING. This build is about to expire. Please write to [email protected] for more information.
# WARNING. This build has expired. Please write to [email protected] for more information.

 --

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anaconda2/envs/mylab3/bin/htmd_babel

parameterise/share/scripts/nonpolar/000-input

htmd_babel.bin

parameterise/share/scripts/nonpolar/scripts

Segmentation Fault with parameterise/share/bin/equiv_atom

In [6]: poses, scores = dock(prot, lig)

2016-06-06 22:37:39,866 - htmd.molecule.molecule - INFO - Attempting PDB query for 2OV5

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