[gmx-users] minimization

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 13 21:18:27 CEST 2009

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



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
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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

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