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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