How to restraining Cu ion in the Enzyme pocket along with ligand during MD Simulations?

User discussions
1

GROMACS version:2020
GROMACS modification:

I am using GROMAC for MD, However I am not able to figure out how to select atoms or residues to apply a harmonic restraint.

At the active site there is a Cu ion and I want it remain there along with surrounding residues, water molecule and ligand so that it stays there in similar conformation during MD run. I don’t want it to fly away.

Is there any way to restrain the atoms and residues within a particular distance from specific atom e.g. copper?

2

Hi,
to apply simple harmonic restrain between two atoms, : use [ bonds ] type 6 in the [ moleculetype ] section in the topology file.

See the following table for the synthax http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#topfile

Best regards
Alessandra