GROMACS version: 5.1.4
GROMACS modification: No
Respected community members, I am doing a protein-ligand simulation using the latest version of Charmm36 port. I have used the CgenFF server to generate the parameters for the ligand. Unfortunately, I am getting very high penalty scores. Infact there are two values given in the .str file. The first is the param penalty which is 158.800 and the second one is the charge penalty (49.851). Param penalty to me appears to be the sum of all charge penalties. I do not understand the other value. In any case I have to do the reparameterization of the ligand before running the simulation. Can some expert in the field help me in getting this job done. I am posting the screenshot of the .str file below for the reference. I found some answers regarding this on ResearchGate; however, I could not find a comprehensive step-by-step tutorial/protocol to get this done. Kindly help me. Thanks in advance.
The 2010 CGenFF paper is itself a tutorial, including all details of how to perform relevant QM calculations (methods and basis sets), water interactions, potential energy scans, etc. There is a slide deck and example inputs as a sort of tutorial on Alex MacKerell’s website (under Force Field Resources), but it’s all very CHARMM-centric. Generating some of the necessary inputs and some of the calculations are not even possible in GROMACS.