Christopher, See this page for more info on this error: http://wiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordi nate_file_does_not_match_topology Jonathan
____________________________ Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office 300E Midland, MI 48674 USA Phone: (989) 636-9765 Fax: (989) 636-4019 E Mail: [EMAIL PROTECTED] -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, July 21, 2007 4:10 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] number of coordinates in coordinate file does not match topology Christopher Stiles wrote: > I get the following when running grompp: > > > > -bash-3.00$ grompp -f mdout_test.mdp -c SWNT_6_6_144.gro -p > SWNT_6_6_144.top -o > > :-) G R O M A C S (-: > > > > God Rules Over Mankind, Animals, Cosmos and Such > > > > :-) 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 mdout_test.mdp Input, Opt! grompp input file with MD parameters > > -po mdout.mdp Output grompp input file with MD parameters > > -c SWNT_6_6_144.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 SWNT_6_6_144.top Input Topology file > > -pp processed.top Output, Opt. Topology file > > -o topol.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.6# > > checking input for internal consistency... > > calling cpp... > > processing topology... > > processing coordinates... > > ------------------------------------------------------- > > Program grompp, VERSION 3.3.1 > > Source code file: grompp.c, line: 448 > > > > Fatal error: > > number of coordinates in coordinate file (SWNT_6_6_144.gro, 144) > > does not match topology (SWNT_6_6_144.top, 0) > > ------------------------------------------------------- > > > > "You're Insignificant" (Tricky) > > > > > > These of the commands I use to get to that point: > > > > x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp > > /***Note: for some reason it does not generate SWNT_6_6_144.rtp/ > > > > editconf -f SWNT_6_6_144.gro -o SWNT_6_6_144.gro -d 0.5 > > > > genbox -cp SWNT_6_6_144.gro -cs -o SWNT_6_6_144_b4em.gro -p > SWNT_6_6_144.top -maxsol 300 > > / / > > grompp -f mdout_test.mdp -c SWNT_6_6_144.gro -p SWNT_6_6_144.top -o > > > > > > Also I notice that after running grompp it over writes the top file with: > > > > # 1 "ffG43b1.n2t" > > # 1 "<built-in>" > > # 1 "<command line>" > > # 1 "ffG43b1.n2t" > > C C 1 C ; CNT Carbon with one bond > > C C 2 C C ; CNT double bonded Carbon > > O O 1 C ; CARBONYL OXYGEN (C=O) > > O OM 1 C ; CARBOXYL OXYGEN (CO-) > > O OA 2 C H ; HYDROXYL OXYGEN (OH) > > O OW 2 H H ; WATER OXYGEN > > N N 3 H C C ; PEPTIDE NITROGEN (N OR NH) > > N NT 3 H H C ; TERMINAL NITROGEN (NH2) > > N NL 4 C H H H ; TERMINAL NITROGEN (NH3) > > N NR5 2 C C ; AROMATIC N (5-RING,2 BONDS) > > N NR5* 3 C C H ; AROMATIC N (5-RING,3 BONDS) > > N NP 3 C C FE ; PORPHYRIN NITROGEN > > C C 3 C O * ; BARE CARBON (PEPTIDE,C=O,C-N) > > ; Note that order is importante here because of wildcards. > > C C3 4 H H H * ; ALIPHATIC CH3 GROUP > > C C2 4 H H C * ; ALIPHATIC CH2 GROUP > > C C1 4 H C * * ; ALIPHATIC CH GROUP > > C CB 3 C C C ; BARE CARBON (5-,6-RING) > > H H 1 N ; HYDROGEN BONDED TO NITROGEN > > H HO 1 O ; HYDROXYL HYDROGEN > > H HW 1 OW ; WATER HYDROGEN > > H HS 1 S ; HYDROGEN BONDED TO SULFUR > > > > > > Any help or advice is greatly appreciated! > read the error message! 0 atoms in your topology means your topology is broken in some way. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list [email protected] 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 _______________________________________________ gmx-users mailing list [email protected] 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
