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 <khab...@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-us...@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-requ...@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 _______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
