On 9/20/13 2:28 AM, Santhosh Kumar Nagarajan wrote:
Hi guys,
The error I'm getting is as follows
"All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 56
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
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)
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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