For an example go to the TEST folder and run:
python ../generate_prms.py -l TEST -FF OPLS2005 -o Q
After the .prm files have been generated you can run:
$QDIR/qprep < Q_TEST.inp > Q_TEST.out
to generate a water solvated system of the TEST.pdb ligand.
Currently OPLS2005 and OPLS2015 protein parameters and OPLS2005 ligand parameters are included. For now only transformation to Q parameters is included, converting to GROMACS .itp files and other forcefield will be added later.
NOTE: the charge group assignment is currently being developed, therefore the user is highly encouraged to check the assigned charge groups for ligands in the .lib file!
- Schrodinger's ffld_server.
- Q