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Dear Anna,<br>
are you talking about a system "in vacuo" or in solvent ? <br>
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.<br>
I do not think it's a ligand problem, BTW.<br>
<br>
Cheers<br>
<br>
Luca<br>
<br>
<br>
<br>
<blockquote cite="mid:72F15A979E724D109CE549C857093212@AnnaNetbook"
type="cite">
<div><span class="062391112-21052010"><font face="Arial" size="2">Dear
gmx-users,</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">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.</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">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:</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">Potential
Energy = -6.07e+5 (for the prot+lig); -5.58e+5 (for the protein alone)</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">Maximum
force = inf on atom 1</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">Norm
of force = inf</font></span></div>
<div><span class="062391112-21052010"></span> </div>
<div><span class="062391112-21052010">
<div><font face="Arial"><font size="2"><span
class="062391112-21052010">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, t</span>he potential energy
seems to be correct (it is negative, and the order of magnitude is
similar to that of other systems I studied before). <span
class="062391112-21052010">U</span>sually 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!!!</font></font> <span
class="062391112-21052010"><font face="Arial" size="2">Moreover, the
same thing happens in both cases, so I don't think it's a problem
related to the ligand.</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">What
do you think about? Could you give me some hint?</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">Thank
you very much and best regards</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">Anna</font></span></div>
</span></div>
<div><font face="Arial" size="2"><span class="062391112-21052010"></span></font> </div>
<div align="left">
<div align="left"><font face="Arial" size="2">__________________________________________________________________</font></div>
<div align="left"><font face="Arial" size="2">Anna Marabotti, Ph.D.</font></div>
<div align="left"><font face="Arial" size="2">Laboratory of
Bioinformatics and Computational Biology</font></div>
<div align="left"><font face="Arial" size="2">Institute of Food
Science - CNR</font></div>
<div align="left"><font face="Arial" size="2">Via Roma, 64</font></div>
<div align="left"><font face="Arial" size="2">83100 Avellino</font></div>
<div align="left"><font face="Arial" size="2">Phone: +39 0825 299651</font></div>
<div align="left"><font face="Arial" size="2">Fax: +39 0825 781585</font></div>
<div align="left"><font face="Arial" size="2">E-mail: <a
moz-do-not-send="true" title="mailto:amarabotti@isa.cnr.it"
href="mailto:amarabotti@isa.cnr.it">amarabotti@isa.cnr.it</a></font></div>
<div align="left"><font face="Arial" size="2">Skype account: annam1972</font></div>
<div align="left"><font face="Arial" size="2">Web site: <a
moz-do-not-send="true"
title="http://bioinformatica.isa.cnr.it/anna/anna.htm"
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</a></font></div>
<div align="left"> </div>
<div align="left"><font face="Arial" size="2">"If you think you're
too small to make a change, try sleeping with a mosquito"</font></div>
</div>
<div> </div>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
........................................................
--
Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:luca.mollica@ibs.fr">luca.mollica@ibs.fr</a> (<a class="moz-txt-link-abbreviated" href="mailto:lucamollica@gmail.com">lucamollica@gmail.com</a>)
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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