[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Fri Sep 8 13:40:33 CEST 2017

On 9/8/17 5:43 AM, abir paul wrote:
> hi,
>         I am very new to gromacs. I want to see phosphorylation effect on a
> protein molecule. So I have phosphorylated my protein in charmm-gui server.
> when i tried to generate .gro file by using pdb2gmx command line it gives
> me following error :
>                Fatal error:
>               Residue 1 named GLY of a molecule in the input file was mapped
>               to an entry in the topology database, but the atom N used in
>               an interaction of type improper in that entry is not found in
> the
>               input file. Perhaps your atom and/or residue naming needs to be
>               fixed.
> How can I fixed this error. please help me.

CHARMM-GUI will build the whole system for you, including generating the 
GROMACS topology and input files.  There's no need to run anything 
through pdb2gmx.



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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