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<P><FONT SIZE=2>Fellow gmx users,<BR>
<BR>
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?<BR>
<BR>
My .itp file is pasted below:<BR>
<BR>
<BR>
<BR>
[ moleculetype ]<BR>
; Name nrexcl<BR>
TFE 3<BR>
<BR>
[ atoms ]<BR>
; nr type resnr residue atom cgnr charge<BR>
1 opls_161 1 TFE C1 1 0.797<BR>
2 opls_164 1 TFE F2 1 -0.285<BR>
3 opls_164 1 TFE F3 1 -0.280<BR>
4 opls_164 1 TFE F4 1 -0.278<BR>
5 opls_160 1 TFE C5 2 -0.033<BR>
6 opls_162 1 TFE O6 3 -0.479<BR>
7 opls_163 1 TFE H7 3 0.292<BR>
8 opls_165 1 TFE H8 2 0.133<BR>
9 opls_165 1 TFE H9 2 0.132<BR>
<BR>
[ bonds ]<BR>
; ai aj funct c0 c1<BR>
1 2 1 0.13570 351456.0 <BR>
1 3 1 0.13570 351456.0 <BR>
1 4 1 0.13570 351456.0 <BR>
1 5 1 0.15100 292880.0<BR>
5 6 1 0.13640 376560.0<BR>
6 7 1 0.09450 462750.4<BR>
5 8 1 0.10900 284512.0<BR>
5 9 1 0.10900 284512.0<BR>
<BR>
[ pairs ]<BR>
<BR>
<BR>
[ angles ]<BR>
; ai aj ak funct c0 c1<BR>
2 1 5 1 109.5 418.4 <BR>
3 1 5 1 109.5 418.4<BR>
4 1 5 1 109.5 418.4<BR>
1 5 8 1 110.7 313.8<BR>
1 5 6 1 109.5 418.4<BR>
1 5 9 1 110.7 313.8<BR>
5 6 7 1 108.5 460.24 <BR>
8 5 9 1 107.8 276.144<BR>
<BR>
[ dihedrals ]<BR>
; ai aj ak al funct c0 c1 c2 c3 c4 c5 <BR>
2 1 5 6 3 1.12968 3.38904 0.00000 -4.51872 0.0000 0.0000 <BR>
3 1 5 6 3 1.12968 3.38904 0.00000 -4.51872 0.0000 0.0000<BR>
4 1 5 6 3 1.12968 3.38904 0.00000 -4.51872 0.0000 0.0000<BR>
1 5 6 7 3 0.26778 -9.36798 9.10020 0.00000 0.0000 0.0000 <BR>
2 1 5 8 3 0.65689 1.97066 0.00000 -2.62755 0.0000 0.0000<BR>
3 1 5 8 3 0.65689 1.97066 0.00000 -2.62755 0.0000 0.0000<BR>
4 1 5 8 3 0.65689 0.97066 0.00000 -2.62755 0.0000 0.0000<BR>
2 1 5 9 3 0.65689 0.97066 0.00000 -2.62755 0.0000 0.0000<BR>
3 1 5 9 3 0.65689 0.97066 0.00000 -2.62755 0.0000 0.0000<BR>
4 1 5 9 3 0.65689 0.97066 0.00000 -2.62755 0.0000 0.0000<BR>
<BR>
[ dihedrals ]<BR>
<BR>
; The force field to be included<BR>
#include "ffoplsaa.itp"<BR>
<BR>
<BR>
<BR>
; Include generic topology for ions<BR>
#include "ions.itp"<BR>
<BR>
<BR>
[ system ]<BR>
<BR>
<BR>
[ molecules ]<BR>
; Compound #mols<BR>
TFE 1<BR>
<BR>
Thank you for any suggestions.<BR>
<BR>
<BR>
Michael Owen<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
Message: 1<BR>
Date: Tue, 10 Oct 2006 00:12:01 +0200<BR>
From: David van der Spoel <spoel@xray.bmc.uu.se><BR>
Subject: Re: [gmx-users] no coordinates in .top file<BR>
To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>
Message-ID: <452AC931.2040008@xray.bmc.uu.se><BR>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<BR>
<BR>
Owen, Michael wrote:<BR>
><BR>
> Fellow gmx users,<BR>
><BR>
> I made a tolopgy file for TFE in water by "hand" for the OPLSAA/L force<BR>
> field to be used in a simulation containing a mixed solvent. I made a<BR>
> similar TFE.itp file and included it in the mixed solvent topology<BR>
> file. when I ran grompp before equilibrating the system I received an<BR>
> error message that read:<BR>
><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>
> Do you know why my topology file contains zero coordinates? My topology<BR>
> file is pasted below:<BR>
<BR>
Topology looks fine, but grompp =will give you more info when you run<BR>
it with -v. Please read carefully what it saya<BR>
--<BR>
David.<BR>
________________________________________________________________________<BR>
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>
Dept. of Cell and Molecular Biology, Uppsala University.<BR>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
phone: 46 18 471 4205 fax: 46 18 511 755<BR>
spoel@xray.bmc.uu.se spoel@gromacs.org <A HREF="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A><BR>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>
<BR>
</FONT>
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