[gmx-users] coarse grain topology file

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Mar 25 09:55:38 CEST 2007

Hi Mark (and Shanshan Qin),

That was the thing that struck me first too, but look closely. The
first statement before the [ molecules ] section is the #include
"CG.itp", and the file CG.itp is given next. Shanshan Qin apparently
pasted both files, and each of these seems to be good by itself (would
have been better to explicitly mention that they were two files).

Shanshan Qin, does grompp give further warnings? In case you've
checked for the windows endline (to show up in linux as ^M) and there
isn't any, maybe you can send me a zip file containing the .top .itp
.mdp and .gro files you used to grompp.



On 3/25/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > Hi,everyone,I put forward the question yesterday.
> > When I run the simulation, the system always echo
> > "Fatal error: number of coordinates in coordinate file (conf.gro, 12032)
> > does not match topology (topol.top, 0)".
> > Mr Abraham has pointed out maybe there is something wrong with the
> > topol.top file.
> > Now I put the topol.top here:
> As I suggested, your topology format is wrong. Please read page 98 of the
> manual, and reconsider the location of your [molecules] section
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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