[gmx-users] Adding residue to .rtp file

Justin Lemkul jalemkul at vt.edu
Wed Oct 10 02:25:59 CEST 2018

On 10/5/18 10:23 AM, Raji wrote:
> Thank you for your reply.
> "stitching an alkyl group to an existing amino acid should be very
> straightforward without having to parametrize the entire molecule"
> Can you please explain me how to do that?

Functional groups can generally be used like building blocks; they're 
very transferable. You can just amend the residue topology to include 
the new moietie(s), balance charges, and you're largely done. There may 
be some missing bonded terms that have to be parametrized or imported by 
analogy, but it's fairly straightforward. With some basic validation 
(see my many past posts on such topics), you can proceed.



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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