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<P><FONT SIZE=2>Hello gmx users,<BR>
<BR>
here is the command that I used to run the preprocessor for my TFE molecule: <BR>
<BR>
grompp -f em -v -o em -c tfe -p tfe_mike.top <BR>
<BR>
<BR>
and the output is pasted below.<BR>
<BR>
:-) G R O M A C S (-:<BR>
<BR>
Go Rough, Oppose Many Angry Chinese Serial killers<BR>
<BR>
:-) VERSION 3.3.1 (-:<BR>
<BR>
<BR>
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<BR>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<BR>
Copyright (c) 2001-2006, The GROMACS development team,<BR>
check out <A HREF="http://www.gromacs.org">http://www.gromacs.org</A> for more information.<BR>
<BR>
This program is free software; you can redistribute it and/or<BR>
modify it under the terms of the GNU General Public License<BR>
as published by the Free Software Foundation; either version 2<BR>
of the License, or (at your option) any later version.<BR>
<BR>
:-) grompp (-:<BR>
<BR>
Option Filename Type Description<BR>
------------------------------------------------------------<BR>
-f em.mdp Input, Opt! grompp input file with MD parameters<BR>
-po mdout.mdp Output grompp input file with MD parameters<BR>
-c tfe.gro Input Generic structure: gro g96 pdb tpr tpb tpa<BR>
xml<BR>
-r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa<BR>
xml<BR>
-rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa<BR>
xml<BR>
-n index.ndx Input, Opt. Index file<BR>
-deshuf deshuf.ndx Output, Opt. Index file<BR>
-p tfe_mike.top Input Topology file<BR>
-pp processed.top Output, Opt. Topology file<BR>
-o em.tpr Output Generic run input: tpr tpb tpa xml<BR>
-t traj.trr Input, Opt. Full precision trajectory: trr trj<BR>
-e ener.edr Input, Opt. Generic energy: edr ene<BR>
<BR>
Option Type Value Description<BR>
------------------------------------------------------<BR>
-[no]h bool no Print help info and quit<BR>
-nice int 0 Set the nicelevel<BR>
-[no]v bool yes Be loud and noisy<BR>
-time real -1 Take frame at or first after this time.<BR>
-np int 1 Generate statusfile for # nodes<BR>
-[no]shuffle bool no Shuffle molecules over nodes<BR>
-[no]sort bool no Sort molecules according to X coordinate<BR>
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<BR>
sites<BR>
-load string Releative load capacity of each node on a<BR>
parallel machine. Be sure to use quotes around<BR>
the string, which should contain a number for<BR>
each node<BR>
-maxwarn int 10 Number of warnings after which input processing<BR>
stops<BR>
-[no]check14 bool no Remove 1-4 interactions without Van der Waals<BR>
-[no]renum bool yes Renumber atomtypes and minimize number of<BR>
atomtypes<BR>
<BR>
creating statusfile for 1 node...<BR>
<BR>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#<BR>
checking input for internal consistency...<BR>
calling /lib/cpp...<BR>
tfe_mike.top:67:1: unterminated #ifdef<BR>
cpp exit code: 256<BR>
Tried to execute: '/lib/cpp -I/usr/local/gromacs/share/gromacs/top -DPOSRE tfe_mike.top > grompppUuhtO'<BR>
The '/lib/cpp' command is defined in the .mdp file<BR>
processing topology...<BR>
Generated 332520 of the 332520 non-bonded parameter combinations<BR>
Generating 1-4 interactions: fudge = 0.5<BR>
Generated 332520 of the 332520 1-4 parameter combinations<BR>
processing coordinates...<BR>
-------------------------------------------------------<BR>
Program grompp, VERSION 3.3.1<BR>
Source code file: grompp.c, line: 448<BR>
<BR>
Fatal error:<BR>
number of coordinates in coordinate file (tfe.gro, 9)<BR>
does not match topology (tfe_mike.top, 0)<BR>
-------------------------------------------------------<BR>
<BR>
"I'm Only Faking When I Get It Right" (Soundgarden)<BR>
<BR>
<BR>
Thank you very muc for your help.<BR>
<BR>
Sincerely,<BR>
<BR>
Michael Owen<BR>
<BR>
<BR>
<BR>
Message: 1<BR>
Date: Tue, 10 Oct 2006 16:59:26 +0200<BR>
From: David van der Spoel <spoel@xray.bmc.uu.se><BR>
Subject: Re: [gmx-users] RE: no coordinates in .top file<BR>
To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>
Message-ID: <452BB54E.80206@xray.bmc.uu.se><BR>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<BR>
<BR>
Owen, Michael wrote:<BR>
> Fellow gmx users,<BR>
><BR>
> thanks for the suggestion, however, applying -v to grompp did not yield<BR>
> any additional information. Shouldn't grompp read the number of<BR>
> coordinates from the list of atoms in the [ atoms ] section? Could<BR>
> something be wrong with my .itp file? Could it be that my .top and .itp<BR>
> files are in my working directory instead of the Gromacs "share" directory?<BR>
><BR>
<BR>
no, the problem is most likely in your topology.<BR>
post the output from grompp -v if you can not find the answer yourself.<BR>
<BR>
<BR>
<BR>
--<BR>
David.<BR>
</FONT>
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