I'm trying to dock my ligand with HEM to CYP using rosetta script with XML protocol
overall running process seems to complete without any problem, and rosetta script seems to recognize HEM and ligand as separate entity
But in some conformer generated by rosetta-script, there is severe clash between HEM and ligand.
For this kind of conformer, rosetta total_score was extremely high and I could filter out this kind of unfavorable structure based on rosetta score
But, Can I set the xml protocol to exclude these kind of conformer generation using rosetta script ?
In xml specification manual and the paper 'RosettaLigand docking with flexible XML protocols', there are many option and specification, but I couldn't find
the information related to reducing the clash between ligand.
Attcached files are
1. structural image which show severe clash between HEM and ligand
2. my protocol xml file used for rosetta script
Any kind of suggestion would be welcomed