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Using specific rotamers

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Using specific rotamers

We're trying to run a docking study between two proteins, with the protein to be docked has a few residues with some rotamers. We want to fix these rotamers, but no matter what we try, Rosetta seems to change the rotamers between the poses. Is there a way for the rotamers to be completely fixed, so that we are docking the same version of the protein in each pose?

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Fri, 2022-08-26 13:45

How to specifiy things depends a bit on the protocol you're using, but in general you can fix the rotamers of sidechains by using the NATRO directive in a resfile (or the equivalent no repack directive if you're using a different method.)

The Meiler Lab protein-protein docking tutorial actually includes an example of fixing such key residues during protein-protein docking (using the PreventResiduesFromRepacking task operation in RosettaScripts). See for more information. If you're using a different protocol, you may need to change how you do that specification.

Fri, 2022-08-26 14:51