If they’re sidechain clashes, repack with fixbb using the membrane scorefunction. If they’re backbone clashes…I guess try relax using the membrane scorefunction? If it’s a Rosetta-generated model, I’d probably just try generating more models with the same protocol in the first place. Which protocol are you using / which paper are you following?
Thank you for replying.
I want to fix sidechain clashes.
I started using the fixbb protocol, with the following command line: fixbb.linuxgccrelease -database /share/apps/rosetta/rosetta_database/ -s test.pdb -packing:repack_only -ex1 -ex2 -extrachi_cutoff 0 -use_input_sc -ndruns 10 -minimize_sidechains -score:weights standard -score:patch no_solvation.
I asked this question since I wasn’t sure if I was using the best rosseta has to offer, however I understand from your response that I was actually using the right thing.
If you want to fix sidechain clashes, this is sufficient for fixing all fixable clashes.
If you want to squeeze another few percent lower energy at the cost of greatly increased runtime, there are more flags you can give to the packer to increase its runtime/rotamer population, but for your stated goal it’s not worth the trouble.