ubuntu:~/down/ssDNA> pdb2gmx -f dna6.pdb -o dna6.gro -ff select :-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description ------------------------------------------------------------ -f dna6.pdb Input Structure file: gro g96 pdb tpr etc. -o dna6.gro Output Structure file: gro g96 pdb etc. -p topol.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -chainsep enum id_or_ter Condition in PDB files when a new chain and molecule_type should be started: id_or_ter, id_and_ter, ter, id or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool no Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool no Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignh bool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000 Force constant for position restraints -vsite enum none Convert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu -[no]chargegrp bool yes Use charge groups in the rtp file -[no]cmap bool yes Use cmap torsions (if enabled in the rtp file) -[no]renum bool no Renumber the residues consecutively in the output -[no]rtpres bool no Use rtp entry names as residue names Select the Force Field: From '/home/majid/soft/gromacs/share/gromacs/top': 1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN force field (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 3 Using the Amber96 force field in directory amber96.ff Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/watermodels.dat Select the Water Model: 1: TIP3P TIP 3-point, recommended 2: TIP4P TIP 4-point 3: TIP4P-Ew TIP 4-point optimized with Ewald 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None 1 Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/aminoacids.r2b Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/dna.r2b Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/rna.r2b Reading dna6.pdb... WARNING: all CONECT records are ignored Read 'UNNAMED', 594 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 14 residues with 594 atoms chain #res #atoms 1 ' ' 14 594 All occupancies are one Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/atomtypes.atp Atomtype 1 Reading residue database... (amber96) Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/aminoacids.rtp Residue 93 Sorting it all out... Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/dna.rtp Residue 109 Sorting it all out... Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/rna.rtp Residue 125 Sorting it all out... Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/aminoacids.hdb Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/dna.hdb Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/rna.hdb Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/aminoacids.n.tdb Opening force field file /home/majid/soft/gromacs/share/gromacs/top/amber96.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.14# Processing chain 1 (594 atoms, 14 residues) There are 0 donors and 7 acceptors There are 0 hydrogen bonds Identified residue DA31 as a starting terminus. Identified residue DT314 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully ------------------------------------------------------- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1017 Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "The Candlelight Was Just Right" (Beastie Boys) ubuntu:~/down/ssDNA>