[gmx-users] how to add distance(and angle) restraint between ligand and protein performing free energy calculation decoupling ligand atoms

[atsutoshi.okabe at takeda.com]

Dear all, 

I'm trying to add distance(angle or orientation) restraint between atoms of ligand and atoms protein(not restraints within ligand or protein) performing free energy calculation decoupling ligand atoms.
To use [distance_restraint] tool between atoms of ligand and protein, I prepared ligand/protein complex topology file compiling parameters of ligand and protein atoms as one [moleculetype]. On the other hand, I know that at 'couple-moltype' in mdp file, I must write [moleculetype] name of only "ligand" at defined in topology file to perform free energy calculation.

So, could you tell me how to add distance restraint between ligand and protein performing free energy calculation decoupling ligand atoms?

Best regards, 
Atsutoshi Okabe