[gmx-users] minimization

[Tsjerk Wassenaar]

Hi Morteza,

I think it will be best for all of us if you can provide the exact
command lines you are using, and the output of pdb2gmx for the
well-performing and an ill-performing force field. Otherwise I'm
afraid that we will not be able to get any further than making
guesses.

Cheers,

Tsjerk

2009/8/13 Morteza Khabiri <khabiri at greentech.cz>:
> Dear MARK and Tsjerk
>
> I found something....after making topology file by pdb2gmx ... I made tpr
> file by grompp ... then I give the original pdb file and tpr file to ngmx
> to see the system before running minimization...the interesting thing was
> that the bonds between atoms are stretched......
> I compare the atoms of amino acids in topology file with the topolgy file
> of other proteins which did not have any problem...the oplss number for
> all atoms is the same....
> but still I could not understand where is the problem....
>
> thanks
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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
>



-- 
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