[gmx-users] number of coordinates in coordinate file does not match topology

Moore, Jonathan (J) JMoore2 at dow.com
Mon Jul 23 14:27:13 CEST 2007


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: jmoore2 at dow.com

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] 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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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