Distance restraints between more than one protein and ligand

User discussions
1

GROMACS version: 2021
GROMACS modification: No

Dear all,

I am simulating a dimeric protein that binds ATP+Mg2+. I would like to use distance restraints for each ATP and Mg2+ molecules and each protein monomer. I cannot set [ bonds ] between them because they are different topology files.

I have read that you can set distance restraints with the pull code. Is it possible to use the pull code for 4 distance restraints? I have only managed to use the pull code for one distance and I am struggling to make it work for more than one.

Thank you very much in advance,

Sara

2

You can add harmonic or flat-bottomed potentials in the [ intermolecular_interactions ] section.