[gmx-users] Fatal Error: Residue 'DMP' not found in residue topology database

Santhosh Kumar Nagarajan santhoshrajan90 at gmail.com
Fri Sep 20 08:28:02 CEST 2013

Hi guys, 
 The error I'm getting is as follows
"All occupancies are one
Opening force field file
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file
Residue 56
Sorting it all out...
Opening force field file
Opening force field file
Opening force field file
Processing chain 1 'A' (46 atoms, 1 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue DMP1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

Program pdb2gmx, VERSION 4.5.3
Source code file: resall.c, line: 581

Fatal error:
Residue 'DMP' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

And this is the command I used

pdb2gmx -f dmpc.pdb -o processed.gro -water spce -ignh

Force field : OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

Help me solve this.
Thanks and Regards

Santhosh Kumar Nagarajan
MTech Bioinformatics
SRM University
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