Input and structure files for the paper "Comparing the performance of different AMBER/GAFF forcefields, partial charge assignments, and water models in absolute binding free energy calculations"
Input files are organized as follows:
- Forcefield parameters are in the "parameters" directory
- Input files are in the directories named by test case: "BRD4", "cMET", and "PDE2A".
- Within each test case directory are the 16 parameter set directories.
- Within each parameter set directory are the ligand directories.
- Within each ligand directory are the python input files, an input directory, an output directory, and a link to the parameters directory
To run the calculations for a given ligand, use the following commands and redirect the output to the output directory as indicated:
- python solvent.py > output/solvent.out
- python restraint.py > output/restraint.out
- python complex.py > output/complex.out
Once all calculations are complete, run the following command:
- python results.py
The results file is named ddG.res. Failed calculations can be restarted as follows:
- python solvent.py recover > output/solvent.out
- python restraint.py recover > output/restraint.out
- python complex.py recover > output/complex.out
Calculations can be extened to longer timescales as follows:
- python solvent.py extend > output/solvent.out
- python restraint.py extend > output/restraint.out
- python complex.py extend > output/complex.out
The python code requires openmm and openmmtools. It is known to work with the following python packages:
openmm 7.4.2 py36_cuda101_rc_1 http://conda.binstar.org/omnia
openmmtools 0.19.0 py36_0 http://conda.binstar.org/omnia
Protein and ligand structure files are in "Structures" directory.
Protein structure : protein.pdb
Ligand structures (AM1-BCC charges): ligands_am1bcc.mol2
Ligand structures (RESP charges): ligands_jaguar.mol2