GROMACS version:
GROMACS modification: Yes/No
Here post your question
2. Is .prm file mandatory for ligand or not ?(In tutorial I found Charmm force field used .prm file but Gromos force field does not used .prm file, so I became confuse)
3… How to correct name error of atom of .pdb file if same atom are named more than two way(like hydrogen atom named as HA1 and HA2) in .rtp file?
The .prm file from CGenFF is just an .itp file, using the CHARMM “parameter file” suffix. It is not mandatory unless the ligand needs parameters that are not already contained in the force field.
All atoms have to have unique names in .rtp entries so that bonded connectivity can be defined unambiguously. Atoms with different names are not, by definition, the “same atom.” They are different atoms.
Thank you for your kind co-operation