I am trying to run matcher with several residue constraints, and have already benchmarked the constraints individually and combined. Problem is that my ligand has several rotamers and once I enable the rotamers consideration in the matcher, the match enumeration makes the run impractical. I could solve this by removing the ligand rotamer consideration for the constraints that don't need it. Is there a way to do this for individual constraints?
Update: based on the source code, you have the option to control the packer for the matching amino acids but not for the ligands hence something like "-enumerate_ligand_rotamers false" will not work. Does anyone know how I could modify the source code for this? Only one of my constraints has a ligand rotamer dependency so an instance in which two different rotamers are found as constraint hits does not happen.