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<DIV><FONT size=2 face=Arial><SPAN class=218544914-31032011>Hi
folks,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=218544914-31032011>I have a problem
with a "strange" residue into a PDB file. It is a cysteinesulfonic acid, in
which the -SH moiety of the Cys residue is replaced by -SO3. This modified
residue is essential for the activity of this protein, therefore I must keep it
into the protein. So, I'm trying to add this new residue to the force field (I'm
planning to use the 43a1ff already modified for lipids in the past). Since I
have Gromacs 4.5.3 I copied the ff directory on my local dir, then I attempted
to modify the aminoacids.rtp file and other files following instructions in the
section "Adding a residue to a force field". In order to have some hints on OCS
topology, I used PRODRG, at least to have some indication on atom, bonds and
angle types, but in the .itp file obtained from PRODRG there are several data
for which I don't find the corresponding element in the ffbonded.itp file. For
example, I don't see any equivalent for the CB - SG - OD1 angle. Probably I
should add them to the ffbonded.itp file, but I'm unsure how to do it. Is
there an order to follow, or can I simply add a new element at the end of the [
angle ] section? Can anyone give me some hint to do it correctly, and more
generally to manage correctly the whole problem? </SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=218544914-31032011>Thanks a
lot</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=218544914-31032011>Anna
Marabotti</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 align=left><FONT size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV></DIV>
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