Hmm, was the OPLSAA run following the GMX one on the dimer or also performed on the monomers? If you feed a multimeric protein without chain identifiers (like in a .gro file) to pdb2gmx, it will bind the different chains together. That would be a good cause for a crash. So I'd say check that first, and check the output from pdb2gmx thoroughly. Also see if you end up with each chain in its own .itp file.
Cheers, Tsjerk 2009/8/13 Mark Abraham <mark.abra...@anu.edu.au>: > Morteza Khabiri wrote: >> >> Dear Tsjerk >> >> Thanks for your suggestion...actually It is a crystal structure...the >> problem happen when I want to minimize the structure in vacuum....the box >> size is enough...but the problem is that the minimization is fine with >> gromacs forcefield but it is not ok with OPLSAA forcefiled.... > > That seems intrinsically improbable, unless the oplsaa .hdb and .tdb files > are not coping with the structure (somehow) and generating a broken starting > configuration and/or topology. What was the final PE and maximum force from > the gromacs forcefield EM? I suggest you look carefully at the post-pdb2gmx > oplsaa structure for steric clashes, unsatisified valences, etc., and then > look at the progress of the corresponding minimization. You should see > evidence of whatever is wrong. > > Mark > >> I tried to >> minimized structure well by gromacs force file and the I took the >> minimized structure from gromacs forcefield and then I tried it in OPLSAA >> and the problem was the same as before... I also cut my structure to some >> pieces ( which I think that it is not reasonable) but I did it but still >> it is not working....and the interesting point is that the protein is >> working by gromacs forcefield well without any problem but when I want to >> use the OPLSAA force field the problem >> start and I could not minimized my system..I also try the AMBER forcefield >> but the AMBER also didi not work and the result was the same as OPLSAA, >> system was exploding.......when I want use all atom the problem appear and >> I really don't know how to manage it..I already tried different coulomb >> type algorythm and also different integrator,, different time >> step..different emtol........but none of them working....... >> >> I would be happy if somebody could suggest me how could I manage it with >> all atom forcefield... >> >> 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 >> > _______________________________________________ > 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
