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Solving van der waals clashes in a transmembrane protein model with rosetta

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Solving van der waals clashes in a transmembrane protein model with rosetta
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Hi,

I was wandering if anyone can tell me what is the best way to resolve van der waals clashes in a model of a transmembrane protein using rosetta?

Thank you,
Doran

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Wed, 2012-12-05 00:12
doranhen

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?

Wed, 2012-12-05 07:59
smlewis

Hi,
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.

Thank you,
Doran

Thu, 2012-12-06 00:29
doranhen

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.

Thu, 2012-12-06 06:39
smlewis