[gmx-users] grommp & coordinate numbers

[David van der Spoel]

On Tue, 2004-11-30 at 16:34 -0800, Bo Yang wrote:
> Hello,Gromacs:
> 
> I try to run the energy minimixzation with my protein
> model. I generated the coordinate files using pdb2gmx
> by chosing '0' force filed, and solvated it using
> 'editconf' (-d 0.5) and 'genbox'. When I try to run
> 'grompp', it complains:
> 
> ----
> processing topology...
> processing coordinates...
> Fatal error: number of coordinates in coordinate file
> (n62.gro, 17981)
what does grompp -v tell you?

apparently something is wrong with the topology, or as you said with
cpp. 
Try the command
which cpp
to find the location of the program. Or use the finder to locate it. 
> 
> does not match topology (n62.top, 0)
> ----
> 
> I checked the mail list. Some one had similar problem.
> But I can't find the answer for it. I am a new user of
> Gromacs. I don't understand the problem presenting
> here. Since the .top and .gro files are generated from
> the same .pdb file. Why they don't have the same
> coordinates numbers. Could any one give me some
> suggestions? 
> 
> Thank you for your help!
> 
> Bo
> 
> 
> 		
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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