[gmx-users] Adding residue to .rtp file
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.
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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