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 "position_restraints 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 them? Best, Steven
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