CTPOL_MD

MD script to run CTPOL model on OpenMM.

Required files:

• Original OPLSAA parameter file, must be named OPLS-AA.xml.
• Input pdb, either as 2nd [optional] argument to script, or a file called input.pdb.

For CTPOL,

• Modified parameter file, 1st argument to script, must have ffaffurr-oplsaa in name.
• A parameter file for CT and Pol, must be named CustomForce.xml

Usage:

python ffaffur-md-1step.py <parameter-file> [pdb]