Author: Tristan Bereau (Max Planck Institute for Polymer Research, Mainz, Germany)
Created: 2014
Automated MARTINI mapping and parametrization of small organic molecules.
For a detailed account of the software, see:
Bereau and Kremer, J Chem Theory Comput, DOI:10.1021/acs.jctc.5b00056 (2015) link
Please consider citing the paper if you find auto_martini
useful in your research.
@article{bereau2015automartini,
author = {Bereau, Tristan and Kremer, Kurt},
title = {Automated parametrization of the coarse-grained MARTINI force field
for small organic molecules},
journal = {J Chem Theory Comput},
year = {2015},
volume = {11},
number = {6},
pages = {2783--2791},
doi = {10.1021/acs.jctc.5b00056}
}
auto-martini
is a python script that requires a number of dependencies:
numpy
: see http://docs.scipy.org/doc/numpy/user/install.htmlrdkit
: see http://www.rdkit.org/docs/Install.htmlbeautifulsoup
: see http://www.crummy.com/software/BeautifulSoup/requests
: see http://docs.python-requests.org/en/latest/user/install/
numpy
and rdkit
can be installed by some package managers. Otherwise you'll have to compile it from source. beautifulsoup
and requests
can easily be installed using pip or easy_install. In case you do not have root access to your computer to install new software, have a look at virtualenv.
Once all the dependencies are correctly installed, a call to the program should return a usage-information message similar to the following:
usage: auto-martini [-h] (--sdf SDF | --smi SMI) --mol MOLNAME [--xyz XYZ]
[--gro GRO] [--verbose] [--fpred]
auto-martini: error: argument --mol is required
To coarse-grain a molecule, simply provide its SMILES code (option --smi SMI
) or a .SDF file (option '--sdf file.sdf
). You also need to provide a name for the CG molecule (not longer than 5 characters) using the --mol
option. For instance, to coarse grain guanazole, you can either obtain/generate (e.g., from Open Babel) an SDF file:
auto-martini --sdf guanazole.sdf --mol GUA
(the name GUA is arbitrary) or use its SMILES code within double quotes
auto-martini --smi "N1=C(N)NN=C1N" --mol GUA
In case no problem arises, it will output the gromacs .itp file:
;;;; GENERATED WITH auto-martini
; INPUT SMILES: N1=C(N)NN=C1N
; Tristan Bereau (2014)
[moleculetype]
; molname nrexcl
GUA 2
[atoms]
; id type resnr residu atom cgnr charge smiles
1 SP2 1 GUA S01 1 0 ; Nc1ncnn1
2 SP2 1 GUA S02 2 0 ; Nc1ncnn1
[constraints]
; i j funct length
1 2 1 0.21
Optionally, the code can also output a corresponding .gro
file for the coarse-grained coordinates
auto-martini --smi "N1=C(N)NN=C1N" --mol GUA --gro gua.gro
Atomistic coordinates can be output in XYZ format using the --xyz output.xyz
option.
Since ALOGPS, the prediction algorithm for octanol/water partitioning, relies on whole fragments rather than individual atoms, the prediction of certain fragments can pose problem, e.g., small inorganic groups. In this case, auto-martini
tries to parametrize alternative mappings. If none of them shows successful, the code will return an error.
; ERROR: no successful mapping found.
; Try running with the '--fpred' and/or '--verbose' options.
As mentioned in the error message, an alternative solution consists of relying on an atom-based partitioning coefficient prediction algorithm (Wildman-Crippen), which is less accurate but can predict any fragment. In case the --fpred
option is selected, only fragments for which ALOGPS fail will be predicted using Wildman-Crippen.
Some versions of Boost will fail to correctly exit at the end of the program, generating such output messages:
python: /usr/include/boost/thread/pthread/mutex.hpp:108: boost::mutex::~mutex(): Assertion `!posix::pthread_mutex_destroy(&m)' failed.
[1] 31433 abort (core dumped) ./auto_martini --smi "N1=C(N)NN=C1N" --mol GUA
the results provided by the code are unaffected by this error message. Simply ignore it.
Older RDKit versions will report the following error:
[...]
distBdAt = Chem.rdMolTransforms.GetBondLength(conf,i,beadId)
AttributeError: 'module' object has no attribute 'GetBondLength'
Simply update your version of RDKit. Most package managers will allow you to do this, unless you've installed RDKit from source.