Docking two inhibitor bound proteins

HADDOCK
1

Hello @amjjbonvin

I want to dock two proteins that are bound to their respective inhibitors.

I understand how to edit the ligand.param and ligand.top files in toppar directory for one ligand, however, I am unable to understand how to deal when I have two ligands.

Any suggestions would be a great help.

Regards
@emartis12

2

Running locally I assume?

You should then combine the two topo/param files into one, make sure there is no overlap in the atom types naming.

1 Like
3

Yes, running locally.

Thanks a ton for the suggestion.

Best regards
@emartis12