Hi, On Friday, 6. July 2007 08:03, [EMAIL PROTECTED] wrote: > Dear gmx users: > I m carrying a protein explicit solvent simulation using gromacs > 3.3, then i added water, but in next step, I m getting the following error,
check your top and gro file, something seriously is wrong, perhaps you have added wrong forcefield in your top file. > > grompp -f em.mdp -c try.gro -p A.top -o A_em.tpr > > :-) G R O M A C S (-: > > Getting the Right Output Means no Artefacts in Calculating Stuff > > :-) VERSION 3.3.1 (-: > > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2006, 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 try.gro Input Generic structure: gro g96 pdb tpr tpb > tpa xml > -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb > tpa xml > -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb > tpa xml > -n index.ndx Input, Opt. Index file > -deshuf deshuf.ndx Output, Opt. Index file > -p A.top Input Topology file > -pp processed.top Output, Opt. Topology file > -o A_em.tpr Output Generic run input: tpr tpb tpa xml > -t traj.trr Input, Opt. Full precision trajectory: trr trj > -e ener.edr Input, Opt. Generic energy: edr ene > > 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]v bool yes Be loud and noisy > -time real -1 Take frame at or first after this time. > -np int 1 Generate statusfile for # nodes > -[no]shuffle bool no Shuffle molecules over nodes > -[no]sort bool no Sort molecules according to X coordinate > -[no]rmvsbds bool yes Remove constant bonded interactions with > virtual sites > -load string Releative load capacity of each node on a > parallel machine. Be sure to use quotes around > the string, which should contain a number for > each node > -maxwarn int 10 Number of warnings after which input processing > stops > -[no]check14 bool no Remove 1-4 interactions without Van der Waals > -[no]renum bool yes Renumber atomtypes and minimize number of > atomtypes > > creating statusfile for 1 node... > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# > checking input for internal consistency... > calling /usr/bin/cpp... > processing topology... > Generated 1284 of the 1485 non-bonded parameter combinations > Cleaning up temporary file grompp3wF5if > ------------------------------------------------------- > Program grompp, VERSION 3.3.1 > Source code file: toputil.c, line: 61 > > Fatal error: > Atomtype 'C3' not found! > ------------------------------------------------------- > > "Baby, It Aint Over Till It's Over" (Lenny Kravitz) > Can you tell me how to correct it? > Best Regards! > Fufeng liu > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
