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<DIV><FONT size=2 face=Arial><SPAN class=343090310-17052010>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=343090310-17052010>is it possible to
minimize a ligand in vacuo, not inserted in a protein, using GROMACS? I tried to
do it using the topology file created by PRODRG server and skipping the pdb2gmx,
editconf, genbox steps, but GROMACS gave me an error indicating that it does not
recognize the moleculetype. The command I used was: </SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=343090310-17052010>grompp -f em.mdp -c
lig.pdb -o ligmin.tpr -o ligtopol_by_PRODRG.top</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=343090310-17052010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=343090310-17052010>I made two attempts:
first, I used the .itp file directly coming from PRODRG, second, I modified this
file by adding the missing infos on my ligand under the different parts [
molecules ], [ systems] and so on. But I was not able to force Gromacs
recognizing my molecule. Obviously, my ligand is not a peptide, but is a small
molecule.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=343090310-17052010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=343090310-17052010>I searched for some
hints in the gmx-users archive and found this message:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=343090310-17052010><A
href="http://lists.gromacs.org/pipermail/gmx-users/2008-October/037164.html">http://lists.gromacs.org/pipermail/gmx-users/2008-October/037164.html</A></SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=343090310-17052010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=343090310-17052010>but it seems to me
that it does not answer to my problem. If I follow the Kerrigan's tutorial, it
indicates how to create a topology for the ligand, but not how to minimize it in
the absence of the protein.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=343090310-17052010>Could you give me a
more clear explanation? Sorry if the request seems to be trivial, but I really
can't understand what to do.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=343090310-17052010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=343090310-17052010>Many thanks in
advance and best regards</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=343090310-17052010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=343090310-17052010>Anna</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></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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