[gmx-users] Adding residue to .rtp file

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 15:17:01 CEST 2018

On 10/3/18 5:15 PM, Raji wrote:
> Hi
> I would like to simulate a peptide, in which  alkyl chain is covalently
> linked with aminoacid. I have generated the topology for alkyl chain with
> CGenFF and converted to CHARMM format. Now how to include this parameters
> in the aminoacid rtp file. If the alkyl chain is bonded with aminoacid TYR,
> do i need to add the alkyl chain parameters with TYR in rtp file as well
> how to represent the bond formation between them.

You shouldn't create a Frankenresidue with part CHARMM parameters and 
part CGenFF. While CHARMM and CGenFF are compatible, the general nature 
of CGenFF means the atom type properties are a tradeoff between accuracy 
and transferability. If you're creating a custom protein residue, use 
core CHARMM atom types, which are more highly optimized for this 
purpose. Linking an alkyl chain should be very straightforward by simply 
adding building blocks together.



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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