[gmx-users] GLY dihedrals in amber03 family force fields

[Tomek Wlodarski]

Thanks Justin.
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...
Best,

tomek

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:
>
>> Hi,
>>
>> 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
>> mapped
>> 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
>> fixed.
>>
>> 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
> mistake.
>
> -Justin
>
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