:-) G R O M A C S (-: Gallium Rubidium Oxygen Manganese Argon Carbon Silicon :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, 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 cpeptide.pdb Input Generic structure: gro g96 pdb tpr tpb tpa xml -o cpeptide.gro Output Generic structure: gro g96 pdb xml -p cpeptide.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -[no]merge bool no Merge chains into one molecule definition -ff string select Force field, interactive by default. Use -h for information. -water enum spc Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c -[no]inter bool no Set the next 6 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 Opening library file /usr/local/packages/gromacs/share/gromacs/top/FF.dat Opening library file /usr/local/packages/gromacs/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/packages/gromacs/share/gromacs/top/aminoacids.dat Opening library file /usr/local/packages/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully All occupancies are one Opening library file /usr/local/packages/gromacs/share/gromacs/top/ffG43a1.atp Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Opening library file /usr/local/packages/gromacs/share/gromacs/top/ffG43a1.rtp Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Sorting it all out... Opening library file /usr/local/packages/gromacs/share/gromacs/top/ffG43a1.hdb Opening library file /usr/local/packages/gromacs/share/gromacs/top/ffG43a1-n.tdb Opening library file /usr/local/packages/gromacs/share/gromacs/top/ffG43a1-c.tdb There are 22 donors and 20 acceptors There are 23 hydrogen bonds Will use HISB for residue 12 Opening library file /usr/local/packages/gromacs/share/gromacs/top/specbond.dat 6 out of 6 lines of specbond.dat converted succesfully Special Atom Distance matrix: HISB12 NE297 MET13 SD104 0.858 Making bonds... Opening library file /usr/local/packages/gromacs/share/gromacs/top/aminoacids.dat Number of bonds was 149, now 144 Generating angles, dihedrals and pairs... Before cleaning: 225 pairs Before cleaning: 258 dihedrals There are 74 dihedrals, 66 impropers, 209 angles 225 pairs, 144 bonds and 0 virtual sites Total mass 1547.779 a.m.u. Total charge 1.000 e Writing topology Writing coordinate file... Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges Reading cpeptide.pdb... Read 108 atoms Analyzing pdb file There are 1 chains and 0 blocks of water and 13 residues with 108 atoms chain #res #atoms 1 ' ' 13 108 Reading residue database... (ffG43a1) Processing chain 1 (108 atoms, 13 residues) Checking for duplicate atoms.... Now there are 107 atoms. Deleted 1 duplicates. N-terminus: NH3+ C-terminus: COO- Now there are 13 residues with 143 atoms --------- PLEASE NOTE ------------ You have succesfully generated a topology from: cpeptide.pdb. The G43a1 force field and the spc water model are used. Note that the default mechanism for selecting a force fields has changed, starting from GROMACS version 3.2.0 --------- ETON ESAELP ------------ gcq#268: "I'm Looking for a New Simulation" (Stone Temple Pilots)