[gmx-users] number of coordinates in coordinate file does not match topology
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jul 21 10:10:06 CEST 2007
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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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