GitHub - jandom/paramchem: Python scrapper for paramche/cgenff server, small molecule parametrization

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Python scrapper for paramche/cgenff server, small molecule parametrization

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Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
examples		examples
LICENSE		LICENSE
README		README
paramchem.py		paramchem.py

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paramchem.py
============


Install
-------

Download the cgenff force-field and python script

http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx.py
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jun2015.ff.tgz


Usage
-----

Example use

cd examples/benzene

python paramchem.py -u "YOUR USERNAME" -p "YOUR PASSWORD" -c benzene.pdb 
# or 
python paramchem.py -u "YOUR USERNAME" -p "YOUR PASSWORD" -c benzene.mol2

# manually correct the "RESI" line in benzene.str to be 
# RESI BNZ 0.000 ! param...

python cgenff_charmm2gmx.py BNZ benzene.mol2 benzene.str charmm36-jun2015.ff/