[gmx-users] Position Restraints of one of the moleculetpye

Steven Neumann s.neumann08 at gmail.com
Mon May 28 16:48:10 CEST 2012

Dear Gmx Users,

I am fighting with the position restraints. My system cosnsists of 6
ligands - all of them have the same topology - ligand.itp. I want to:

1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L,
posre ligand1.itp
2. Restrain 5 of them and pull one of them away.

Here I came across some difficulties.

I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp

and by index files I create an index of the ligands I wan to restrain. Each
my ligands has 46 atoms. When I process to grompp:

Atom index (256) in position_restraints out of bounds (1-46).
This probably means that you have inserted topology section

Shall I rename Ligands as different residue names? If my posre includes
1-46 atom all ligands are restraints? How to restrain just 5 out of 6 of


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