[gmx-users] amber ff gromacs

[Mark Abraham]

Amber forcefields use terminal residues that are  parametrized differently
from normal ones. You can't just label a few atoms as the terminal ones and
have it work; you need a whole residue, and this makes a single-residue
zwitterion topology impossible to build with pdb2gmx. You need to cap the
termini, or use two residues, or some other topology building tool.

Mark
On Mar 24, 2014 8:26 AM, "virk" <virkblitz at yahoo.com> wrote:

> Dear People,
>
> I am trying to simulate glycine molecule using amber ff. I have changed the
> residues in pdb file with N and C respectively.
> ATOM      1  N    NGLY    1      -1.476   0.232   0.252  1.00  0.00
> ATOM      2  CA  CGLY    1      -0.012   0.296   0.348  1.00  0.00
> ATOM      3  C    CGLY    1       0.596  -0.652  -0.648  1.00  0.00
> ATOM      4  O     GLY     1      -0.124  -1.320  -1.368  1.00  0.00
> ATOM      5  OXT GLY     1       1.916  -0.760  -0.740  1.00  0.00
> ATOM      6  H3   GLY     1      -1.736  -0.252  -0.592  1.00  0.00
> ATOM      7  HA2 GLY     1       0.292   0.020   1.364  1.00  0.00
> ATOM      8  HA1 GLY     1       0.320   1.320   0.132  1.00  0.00
> ATOM      9  H    GLY     1      -1.636  -0.236   1.132  1.00  0.00
> ATOM     10  H   GLY     1      -1.916   1.136   0.272  1.00  0.00
> TER      11         GLY     1
> END
>
> But when I am using pdb2gmx, I am getting this error
> Residue 1 named NGLY of a molecule in the input file was mapped to an entry
> in the topology database, but the atom CA used in that entry is not found
> in
> the input file.
>
> But atom CA is in the input pdb file and with same name in amber .rtp file
> too. If I remove N and C prefixes in pdb file, pdb works for all other
> fields.
>
> I will be thankful for your help and time.
>
> Kind Regards,
> Amninder Virk
>
>
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