[gmx-users] A problem with grompp
ksr at chemistry.umass.edu
Fri Dec 15 18:51:26 CET 2006
These problems are typically due to grompp not finding cpp (make sure
it's in your path) or having opened the top file in some non-linux
text editor. Open the top file in vi and see if you see 'M^' where
you would expect line breaks. If so your top file is polluted. To
change from mac line breaks to unix use:
tr '\015' '\012' <bad.top> fixed.top
Where '\015' is the mac line break and '\012' is the unix. If it's a
windows prob. you'll have to google for the windows line break code.
I have had occasions where the above did not fix the solution, very
frustrating. If nether of the above fix the problem just re-create
your .mdp file in vi, this always fixes this problem.
On Dec 15, 2006, at 12:22 PM, David van der Spoel wrote:
> Александр Журавлев wrote:
>> A problem with Gromacs-3.3: When I try ty run grompp using a.gro
>> and a.top files, system says that number of coordinates in a.gro,
>> 440, does not match number of coordinates in a.top, 0. That's
>> strange because the both files were converted by pdb2gmx from one:
>> a.pdb. Maybe it's necessary to specify number of atoms somewhere
>> in a.top file? _______________________________________________
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> please check the output from pdb2gmx again, and also the top file.
> There is most likely an error there.
> 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://folding.bmc.uu.se
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
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