[gmx-users] Adding residue to .rtp file

[Justin Lemkul]

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

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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
http://www.thelemkullab.com

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