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<DIV><SPAN class=062391112-21052010><FONT size=2 face=Arial>Dear
gmx-users,</FONT></SPAN></DIV>
<DIV><SPAN class=062391112-21052010><FONT size=2 face=Arial>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 size=2 face=Arial>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 size=2 face=Arial>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 size=2 face=Arial>Maximum force
=
inf on atom 1</FONT></SPAN></DIV>
<DIV><SPAN class=062391112-21052010><FONT size=2 face=Arial>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
size=2 face=Arial>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><SPAN class=062391112-21052010><FONT size=2 face=Arial>What do you
think about? Could you give me some hint?</FONT></SPAN></DIV>
<DIV><SPAN class=062391112-21052010><FONT size=2 face=Arial>Thank you very much
and best regards</FONT></SPAN></DIV>
<DIV><SPAN class=062391112-21052010><FONT size=2
face=Arial>Anna</FONT></SPAN></DIV></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=062391112-21052010></SPAN></FONT> </DIV>
<DIV align=left>
<DIV align=left><FONT size=2
face=Arial>__________________________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science -
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>E-mail: <A
title=mailto:amarabotti@isa.cnr.it
href="mailto:amarabotti@isa.cnr.it">amarabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web site: <A
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><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"If you think you're too small to make a
change, try sleeping with a mosquito"</FONT></DIV></DIV>
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