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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
