:-) G R O M A C S (-: S C A M O R G :-) VERSION 4.0.3 (-: 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. :-) grompp (-: Option Filename Type Description ------------------------------------------------------------ -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c pblgsolv.gro Input Structure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p pblg.top Input Topology file -pp processed.top Output, Opt. Topology file -o minimpept.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 334153 of the 334153 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 334153 of the 334153 1-4 parameter combinations ERROR 1 [file pblg.top, line 202]: No default Bond types ERROR 2 [file pblg.top, line 203]: No default Bond types ERROR 3 [file pblg.top, line 783]: No default Angle types ERROR 4 [file pblg.top, line 784]: No default Angle types ERROR 5 [file pblg.top, line 805]: No default Angle types ERROR 6 [file pblg.top, line 807]: No default Angle types ERROR 7 [file pblg.top, line 808]: No default Angle types ERROR 8 [file pblg.top, line 809]: No default Angle types ERROR 9 [file pblg.top, line 810]: No default Angle types ERROR 10 [file pblg.top, line 811]: No default Angle types ERROR 11 [file pblg.top, line 857]: No default Angle types ERROR 12 [file pblg.top, line 904]: No default Angle types ERROR 13 [file pblg.top, line 951]: No default Angle types ERROR 14 [file pblg.top, line 998]: No default Angle types ERROR 15 [file pblg.top, line 1045]: No default Angle types ERROR 16 [file pblg.top, line 1073]: No default Ryckaert-Bell. types ERROR 17 [file pblg.top, line 1074]: No default Ryckaert-Bell. types ERROR 18 [file pblg.top, line 1075]: No default Ryckaert-Bell. types ERROR 19 [file pblg.top, line 1076]: No default Ryckaert-Bell. types ERROR 20 [file pblg.top, line 1083]: No default Ryckaert-Bell. types ERROR 21 [file pblg.top, line 1084]: No default Ryckaert-Bell. types ERROR 22 [file pblg.top, line 1085]: No default Ryckaert-Bell. types ERROR 23 [file pblg.top, line 1086]: No default Ryckaert-Bell. types ERROR 24 [file pblg.top, line 1087]: No default Ryckaert-Bell. types ERROR 25 [file pblg.top, line 1088]: No default Ryckaert-Bell. types ERROR 26 [file pblg.top, line 1106]: No default Ryckaert-Bell. types ERROR 27 [file pblg.top, line 1120]: No default Ryckaert-Bell. types ERROR 28 [file pblg.top, line 1121]: No default Ryckaert-Bell. types ERROR 29 [file pblg.top, line 1122]: No default Ryckaert-Bell. types ERROR 30 [file pblg.top, line 1123]: No default Ryckaert-Bell. types ERROR 31 [file pblg.top, line 1181]: No default Ryckaert-Bell. types ERROR 32 [file pblg.top, line 1195]: No default Ryckaert-Bell. types ERROR 33 [file pblg.top, line 1196]: No default Ryckaert-Bell. types ERROR 34 [file pblg.top, line 1250]: No default Ryckaert-Bell. types ERROR 35 [file pblg.top, line 1264]: No default Ryckaert-Bell. types ERROR 36 [file pblg.top, line 1265]: No default Ryckaert-Bell. types ERROR 37 [file pblg.top, line 1319]: No default Ryckaert-Bell. types ERROR 38 [file pblg.top, line 1333]: No default Ryckaert-Bell. types ERROR 39 [file pblg.top, line 1334]: No default Ryckaert-Bell. types ERROR 40 [file pblg.top, line 1388]: No default Ryckaert-Bell. types ERROR 41 [file pblg.top, line 1402]: No default Ryckaert-Bell. types ERROR 42 [file pblg.top, line 1403]: No default Ryckaert-Bell. types ERROR 43 [file pblg.top, line 1457]: No default Ryckaert-Bell. types ERROR 44 [file pblg.top, line 1471]: No default Ryckaert-Bell. types ERROR 45 [file pblg.top, line 1472]: No default Ryckaert-Bell. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' NOTE 1 [file pblg.top, line 1582]: System has non-zero total charge: -6.000001e-01 processing coordinates... ------------------------------------------------------- Program grompp, VERSION 4.0.3 Source code file: grompp.c, line: 362 Fatal error: number of coordinates in coordinate file (pblgsolv.gro, 649) does not match topology (pblg.top, 177) ------------------------------------------------------- "Lets Kill the Fucking Band" (Tom Savini - From Dusk til Dawn)