[gmx-users] Fwd: pdb2gmx command

[David van der Spoel]

On 2010-03-07 12.23, bharat gupta wrote:
> Hi all,
>
> I have modelled a protein with one residue as formylated glycine which
> is the active site residue of my protein and when I am running the
> pdb2gmx command I am getting the following error :-
>
> Back Off! I just backed up npep.top to ./#npep.top.4#
> Processing chain 1 (2862 atoms, 358 residues)
> There are 563 donors and 534 acceptors
> There are 758 hydrogen bonds
> Will use HISB for residue 37
> Will use HISB for residue 61
> Will use HISB for residue 63
> Will use HISB for residue 81
> Will use HISB for residue 142
> Will use HISB for residue 172
> Will use HISB for residue 181
> Will use HISB for residue 185
> Will use HISB for residue 204
> Will use HISB for residue 218
> Will use HISB for residue 231
> Will use HISB for residue 277
> Will use HISB for residue 280
> Will use HISB for residue 317
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.7
> Source code file: resall.c, line: 426
>
> Fatal error:
> Residue 'DDZ' not found in residue topology database
>
> ----------------------------------------------
>
> DDZ is the name of that formylated glycine ..

Youneed to (parameterize) and add such a residue to the force field 
(.rtp / .hdb) files. Check chapter 5 in the manual.

>
> So can anybody tell how can I run this .. and what changes do I have
> to make to complete the simulation successfully ..
>
> Please reply ASAP
>
> Thanks
>
>
> --
> Bharat
> M.Sc. Bioinformatics (Final year)
> Centre for Bioinformatics
> Pondicherry University
> Puducherry
> India
> Mob. +919962670525
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se