[gmx-users] (no subject)

[Justin Lemkul]

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

-- 
==================================================

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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