<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content="text/html; charset=us-ascii" http-equiv=Content-Type>
<META name=GENERATOR content="MSHTML 8.00.6001.18999"></HEAD>
<BODY>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>Dear
all,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>I would like to do a
position restraint MD by applying position restraints not only to my
protein but also to its ligand. In order to do it, I created with
genrestr a new protligposre.itp file in which I indicated the group to be
restrained as Protein_lig. In this protligposre.itp file, therefore, there are
restraints on the protein and on the ligand together.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>Then, I modified the
.top file in order to include the statement for the position restraints. I tried
to modify first the usual statement:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>#ifdef
POSRES</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>#include
'posre.itp'</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011>#endif</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><SPAN class=796153510-18022011><FONT size=2
face=Arial>to</FONT></SPAN></DIV>
<DIV><SPAN class=796153510-18022011><FONT size=2
face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN class=796153510-18022011><FONT size=2 face=Arial>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>#ifdef
POSRES_PROTLIG</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>#include
'protligposre.itp'</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011>#endif</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>(obviously, in my
.mdp file I have the statement define = -DPOSRES_PROTLIG)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>Since it did not
work, I used:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011><SPAN
class=796153510-18022011><FONT size=2 face=Arial>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>#ifdef
POSRES</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>#include
"protligposre.itp"</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011>#endif</SPAN></FONT></DIV></FONT></SPAN></SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>(obviously, the
statement in the .mdp file was modified to -DPOSRES)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>Then, I tried
to ADD (not to replace) a new </SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011><SPAN
class=796153510-18022011><FONT size=2 face=Arial>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>#ifdef
POSRES_PROTLIG</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>#include
"protligposre.itp"</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011>#endif</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>and I tried all the
positions in the .top file. </SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>Every time, I
obtained an error stating:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>Fatal error:
</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>[file
protligposre.itp, line 2822 (this number changes every time I change the
position of the statement in the .top file)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>Atom index (2818) in
position_restraints out of bounds (1-2817).</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>This probably means
that you have inserted topology section "position_restraints" in a part
belonging to a different molecule that you intended to. In that case, move the
"position_restraints" section to the right molecule.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>I really don't know
what is the correct position for this statement, since I tried all position that
I could, starting just below the already present statement!</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>Moreover, another
doubt I have is: is it correct to include protein and ligand in the same
posre.itp file? In case it is not correct, what is the correct position in the
.top file to insert the ligposre.itp file (the file containing position
restraints for ligand only)? Please consider that in my .top file the topology
of the ligand was added with the statement</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>#include
"lig.itp"</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>just below the
statement for the forcefield.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796153510-18022011>Thank you very
much</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011>Anna</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796153510-18022011></SPAN></FONT> </DIV></FONT></SPAN></SPAN></FONT></DIV>
<DIV></FONT></SPAN><FONT size=2
face=Arial>__________________________________________________________________</FONT></DIV></DIV>
<DIV align=left>
<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>
<DIV> </DIV></BODY></HTML>