[gmx-users] Adding residue to .rtp file

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 17:36:33 CEST 2018

On 10/4/18 11:28 AM, Raji wrote:
> Thank you for your reply. I am trying to simulate this peptide in gromacs
> with CHARMM36 force field. Thatswhy i converted the parameters from CGenFF
> to CHARMM format. So How to proceed further.  I assume i cant treat it like

The first step is to not use CGenFF to parametrize the custom residue.

> as a protein ligand complex, because there is covalent bond between TYR and
It's just a protein, there is no ligand.

> alkyl chain? And What is core CHARMM atom types?

By "core CHARMM atom types," I mean those that are already part of the 
C36 force field, not coming from CGenFF. If the second character of the 
atom type is "G" then you are using a CGenFF type. Don't.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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