Hybrid molecule topologies for intermolecular distance restraints

User discussions
1

GROMACS version: 2022
GROMACS modification: Yes/No

I want to use intermolecular distance restraints for a simulation involving two protein chains and a ligand. The distance restraints are between protein 1 and ligand, and protein 2 and ligand.

I saw that the distance restraints of type 10 (flat bottom harmonic) need to be intramolecular, and one possible suggestion is to create a topology with a hybrid molecule

My workflow to create the original topology uses amber, then converts to a gromacs topology

Could I use pdb2gmx to merge molecules in an existing gromacs topology, or do I need to do the whole ternary complex preparation using pdb2gmx? Would someone post an example of using pdb2gmx with the merge option?

2

I don’t understand what you mean with “hybrid molecule topology”.

But you I think you should be able to add restraints of type 10 in the intermolecular_interactions section. Then you can have the two molecules in seperate molecule types.