Scripting paramchem.org access
Below is a simple python script that allows one to programatically access paramchem.org, a small-molecule parametrization service. Autocorrect said "problematic" instead of "programatic", maybe I'm noting getting the hint...
The script has minimal dependencies and is very "light-weight", meaning no error handling or error messages. A full working example for a benzene (duh!) is attached.
Long time ago, I had to implement something similar to this script, so this was a fairly easy job. It relies on mechanize and beautiful soup to do it's thing.
python paramchem.py -u "YOUR USERNAME" -p "YOUR PASSWORD" -c benzene.pdb
# 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/
Source code and examples
git clone https://github.com/jandom/paramchem
Example on google drive
Edited: note on errors, link to github repo
The script has minimal dependencies and is very "light-weight", meaning no error handling or error messages. A full working example for a benzene (duh!) is attached.
Long time ago, I had to implement something similar to this script, so this was a fairly easy job. It relies on mechanize and beautiful soup to do it's thing.
python paramchem.py -u "YOUR USERNAME" -p "YOUR PASSWORD" -c benzene.pdb
# 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/
Source code and examples
git clone https://github.com/jandom/paramchem
Example on google drive
Edited: note on errors, link to github repo