How can I keep Cu fixed in protein during the MD simulation?

GROMACS version:2020
GROMACS modification: No

Hello all.I performed an MD simulation on a laccase containing 4 Cu ions in water solvent without any substrate.
simulation run without any error, but when i used vmd for visualizing the last trajectory, one of the ions that was complexed by His and cys, has changed its place and is not inside the protein at the end of simulation time. Is this simulation reliable or not? how can i keep cu fixed in protein during the MD simulation?
I used charmm-gui to generate input files for simulation.

thank you.

Hi,

You can apply harmonic restraint to restrain the distance between the Cu ions and the protein atoms to which they are coordinated

For harmonic restraints you can use [bonds] type 6 in the topology file

See for more details “Distance restraint” in
https://manual.gromacs.org/current/reference-manual/functions/restraints.html?highlight=distance%20restrain

and topology syntax in
http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#topfile

Best regards
Alessandra

Hi @alevilla
I have same problem but with zn ion between 3 cys
I tried add these lines at the end of [bonds]
4954 2989 6
4954 3036 6
4954 3534 6
First atom number is zn and second is cysteines HG

But in the grompp I face the error:
Fatal error:
Invalid pairs type 6

Where is my mistake and how can I solve this?

Hi,
From the error it looks that the values are located in the [pairs] directive, and not in the [bonds] directive. Can you check that the lines are added at the end of the [bonds] directive?
You also need to specify the values of distance b0(nm) and the force [ kJ(mol)-1(nm)-2 ], you want. As a distance you will use the distance between the Zn and S.

Alessandra