[gmx-users] Help

Maryam Nikoosaleh nikoosaleh at ibb.ut.ac.ir
Sun Jul 6 16:15:42 CEST 2008

Dear all,
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 :
"Atom index (821) in constraints out of bounds (1-1).
This probably means that you have inserted topology section "constraints"
in a part belonging to a different molecule than you intended to.
In that case move the "constraints" section to the right molecule."

I don't want to freez this part of protein,b/c I  want to optimize this part 
of protein.
please answer me.
Thnaks , Maryam
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