[gmx-users] Fwd: pdb2gmx command

[bharat gupta]

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 ..

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



-- 
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Puducherry
India
Mob. +919962670525