Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from "Automated Topology Builder" and saved in the root /usr/share/gromacs/top/gromos53a6.ff
I use the next comand i order to convert the pdb format to .gro : *********************************************************************************************************************************** bash >> g_pdb2gmx -f tolu.pdb -o tolu.gro -i tolu.itp Select the Force Field: >From '/usr/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR 13 Using the Gromos53a6 force field in directory gromos53a6.ff Opening force field file /usr/share/gromacs/top/gromos53a6.ff/watermodels.dat Select the Water Model: 1: SPC simple point charge, recommended 2: SPC/E extended simple point charge 3: None 3 Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading tolu.pdb... WARNING: all CONECT records are ignored Read 'ALL ATOM STRUCTURE FOR MOLECULE 0', 15 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 0 residues with 15 atoms chain #res #atoms 1 ' ' 1 15 All occupancies are one Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.7# Processing chain 1 (15 atoms, 1 residues) Warning: Starting residue _I0L0 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 g_pdb2gmx, VERSION 4.5.7 Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/kernel/resall.c, line: 581 Fatal error: Residue '_I0L' 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 ------------------------------------------------------- "You Own the Sun" (Throwing Muses) ************************************************************************************************************************* I checked the residue "_I0L" and is defined in the tolu.itp Why do I get this error? Am I missing something?? Thanks in advance!! Sergio -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013044.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.