[gmx-users] GLY dihedrals in amber03 family force fields
tomek.wlodarski at gmail.com
Wed Oct 29 13:42:53 CET 2014
Yes I know that GLY does not have CB :) that is why I was perplexed with
this - especially it is both in amber03 and amber03w files...
On Wed, Oct 29, 2014 at 12:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 10/29/14 8:35 AM, Tomek Wlodarski wrote:
>> I looked into amber03w topology file for amino acids and I found that GLY
>> has interesting dihedral defined:
>> -C N CA CB
>> Which gives me warnings with pdb2gmx:
>> WARNING: WARNING: Residue 75 named GLY of a molecule in the input file was
>> to an entry in the topology database, but the atom CB used in
>> an interaction of type dihedral in that entry is not found in the
>> input file. Perhaps your atom and/or residue naming needs to be
>> I looked into amber03 main paper but I have not found anything related...
>> Any idea why this dihedral is defined for GLY?
> Glycine doesn't have a beta carbon. Whoever created that file made a
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
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