[gmx-users] A problem with grompp

[Ken Rotondi]

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?    _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the www  
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 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
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> ++++
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20061215/df2ed549/attachment.html>