Dear Anna,
are you talking about a system "in vacuo" or in solvent ?
If you have placed the protein in water w/o minimizing it before
solvation, probabily an "in vacuo" minimization could be useful for your
system before moving into the solvated case. Moreover, are you sure that
the protein does not have "broken" residue or something like that ?
Sometimes, the completion of topology creation step goes fine but
something wrong (on the gromacs side, apart from visualization) with
sidechains or portion of the proteins that are generated by other
softwares/servers.
I do not think it's a ligand problem, BTW.
Cheers
Luca
Dear gmx-users,
I tried to minimize my systems formed by a protein obtained by
homology modelling procedure, in one case with a ligand inside, in the
other case in the apo form.
All worked fine until the minimization step: when I launched mdrun,
the well known "stepsize too small..." communication appears. The
program worked for 37 steps without producing output energies, and the
final report was:
Potential Energy = -6.07e+5 (for the prot+lig); -5.58e+5 (for the
protein alone)
Maximum force = inf on atom 1
Norm of force = inf
I had a look to the gmx-user list archive, but when the "stepsize too
small" error is reported, generally the potential energy is very high.
In my case, the potential energy seems to be correct (it is negative,
and the order of magnitude is similar to that of other systems I
studied before). Usually when I retrieve this error, either the
potential energy is very positive and high, or there are errors in the
protein, but I visualized the systems with VMD and they seem to be
correct. It would sound VERY strange if I had the protein already in a
minimum of potential energy!!! Moreover, the same thing happens in
both cases, so I don't think it's a problem related to the ligand.
What do you think about? Could you give me some hint?
Thank you very much and best regards
Anna
__________________________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabo...@isa.cnr.it <mailto:amarabo...@isa.cnr.it>
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"If you think you're too small to make a change, try sleeping with a
mosquito"
--
........................................................
--
Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France
E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)
Telephone: +33.438783889
--
Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of
cigarettes, it's dark, and we're wearing sunglasses.
Jake: Hit it.
(The Blues Brothers)
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