Obtaining CHARMM input files for GROMACS

User discussions
1

GROMACS version: 2020
GROMACS modification: No

Hello,

I am trying to run a simple benzene simulation using the CHARMM forcefield.
I managed to run a benzene simulation using GROMOS54A7_atb using a .itp and structure file from the Automated Topology Builder. However, if I have a simple benzene pdb file which I made from Avogadro, how would I produce the .itp file I need to run the benzene simulation using GROMACS?

Extrapolating from this, if I needed to run a simulation using some other force-field on GROMACS, for example, OPLS, how would I go about that?

Apologies if this is a basic question, I am still trying to figure out the workings of GROMACS.

2

CHARMM36 supports benzene (residue name BENZ in the .rtp file) so just set the residue name to BENZ in the input coordinate file and rename atoms as needed to match the .rtp entry.

For other force fields, similar servers may exist (e.g. LigParGen for OPLS) but you can easily make an .rtp entry by simply looking at e.g. PHE and porting the charges and atom types to make benzene.