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<DIV><FONT size=2 face=Arial><SPAN class=000502609-10032011>Dear
all,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=000502609-10032011>I have a PDB file of
a protein that is in dimeric form, with an INTERchain disulphide bridge.
However, in their paper the crystallographers are not sure if this is a true
dimeric form or a cyrstallographic artefact (PQS server suggests it is a true
dimeric form, but with low confidence). I'm preparing this protein to do MD
simulations in water, so I used pdb2gmx, editconf, genbox, genion..and all
worked properly (no error messages). Then I launched grompp+mdrun to do a mild
minimization before MD: all worked properly with no error messages, but when I
had a look at the final .gro file, I saw that the disulphide bridge was broken
(before this step, it was present). Looking at the trajectory, I found that the
bridge broke at the first step of the minimization. However, I did not have any
error message, the minimization worked regularly.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=000502609-10032011>I would like to know
if my starting structure is a real dimeric structure, or not, therefore I would
like to know if the disulphide bridge broke because it is only an artefact, or
not. Do I have to add some special constraints to the topology and/or .mdp file
in order to preserve the disulphide bridge in "normal" simulations, or not? I
had a look in the gmx-users list, but I only see suggestions to introduce a new
disulphide bridge (and the messages seem quite old, probably referred to the
Gromacs 3 version, whereas I'm currently using version 4.0.3). In a very
old message (2001) there is the statement "pdb2gmx can *not* make
inter-molecular bonds" however, in this case, the bond is already present in the
crystal and is kept in all phases until the minimization. I tried to use pdb2gmx
-ss in order to set interactively the SS bridge selection, but nothing happened:
the program does not ask me any prompt. Any
suggestions?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=000502609-10032011>Many thanks and best
regards</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=000502609-10032011>Anna
Marabotti</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=000502609-10032011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=000502609-10032011>PS BTW: often when
I'm searching in the gmx-users list I see the suggestions to some links (for
example in the message in <A
href="http://lists.gromacs.org/pipermail/gmx-users/2008-March/032662.html">http://lists.gromacs.org/pipermail/gmx-users/2008-March/032662.html</A>
Mark Abraham suggests to explore <A
href="http://wiki.gromacs.org/index.php/specbond.dat">http://wiki.gromacs.org/index.php/specbond.dat</A>
but when I click on the link, I am redirected to the <A
href="http://www.gromacs.org">www.gromacs.org</A> website. Even if I copy the
link directly in a new browser window, I cannot see the original link.
Why?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left>
<DIV dir=ltr 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>"When a man with a gun meets a man with
a pen, the man with the gun is a dead man"</FONT></DIV></DIV>
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