How to put distance restraints into topology file

User discussions
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1

Hi everyone,

I am trying to restrain the distance between two atoms in a molecule, with just 102 atoms. To be more specific, I want to restrain a MG (number 22) from Chlorophyll with a carbon atom (number 14) from Histidine, to make sure, that their bond stays at the same distance in an optimization. Can some provide an example, of how I can define the restraint in [molecule type]? My topology file ist contained in the following:
acpype_newbondCLAHIS.top (74.9 KB)

2

One way is to add intermolecular interactions to your topology. See if Imposing restraints between protein and ligand and https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html helps.

The other alternative is to use the pull settings in the mdp file, see https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#com-pulling and https://manual.gromacs.org/current/reference-manual/special/pulling.html.

3

Thank you so much, it has worked!

4

I’m glad to hear that!