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<font style="font-family: tahoma; font-size: 10pt;"><p style="font-family:
tahoma; font-size: 10pt;">Dear all,</div><div>I have a question about
restraint. How can I restrain the ligand of one protein? I know how to
restrain atoms of one protein.But when protein has several ligands,
gmx genaretes different *.itp files for their
topologies and when I enter restraints in topology file , gmx gives me this
error : </div><div>"Atom index (821) in constraints out of bounds
(1-1).</div><div>This probably means that you have inserted topology section
"constraints"<br>in a part belonging to a different molecule than you
intended to.<br>In that case move the "constraints" section to the right
molecule."</div><div> </div><div>I don't want to freez this part of
protein,b/c I want to optimize this part of protein.</div><div>please
answer me.</div><div>Thnaks , Maryam </div><div> <br> </div>
<p style="font-family: tahoma; font-size: 10pt;"> </div><p
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