[gmx-users] no coordinates in .top file
Owen, Michael
MichaelOwen at creighton.edu
Tue Oct 10 20:36:57 CEST 2006
Hello gmx users,
here is the command that I used to run the preprocessor for my TFE molecule:
grompp -f em -v -o em -c tfe -p tfe_mike.top
and the output is pasted below.
:-) G R O M A C S (-:
Go Rough, Oppose Many Angry Chinese Serial killers
:-) 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 tfe.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 tfe_mike.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o 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
-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.20#
checking input for internal consistency...
calling /lib/cpp...
tfe_mike.top:67:1: unterminated #ifdef
cpp exit code: 256
Tried to execute: '/lib/cpp -I/usr/local/gromacs/share/gromacs/top -DPOSRE tfe_mike.top > grompppUuhtO'
The '/lib/cpp' command is defined in the .mdp file
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448
Fatal error:
number of coordinates in coordinate file (tfe.gro, 9)
does not match topology (tfe_mike.top, 0)
-------------------------------------------------------
"I'm Only Faking When I Get It Right" (Soundgarden)
Thank you very muc for your help.
Sincerely,
Michael Owen
Message: 1
Date: Tue, 10 Oct 2006 16:59:26 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] RE: no coordinates in .top file
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <452BB54E.80206 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Owen, Michael wrote:
> Fellow gmx users,
>
> thanks for the suggestion, however, applying -v to grompp did not yield
> any additional information. Shouldn't grompp read the number of
> coordinates from the list of atoms in the [ atoms ] section? Could
> something be wrong with my .itp file? Could it be that my .top and .itp
> files are in my working directory instead of the Gromacs "share" directory?
>
no, the problem is most likely in your topology.
post the output from grompp -v if you can not find the answer yourself.
--
David.
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