tsjerkw at gmail.com
Thu Aug 13 15:46:33 CEST 2009
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
2009/8/13 Mark Abraham <Mark.Abraham at 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.
>> 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...
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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