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.
Good luck,
Ken
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.
______________________________________________________________________
__
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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