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) Help me solve this. Thanks and Regards Santhosh. ----- Santhosh Kumar Nagarajan MTech Bioinformatics SRM University Chennai India -- View this message in context: http://gromacs.5086.x6.nabble.com/Fatal-Error-Residue-DMP-not-found-in-residue-topology-database-tp5011333.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
