When running fixbb design runs I tend to find I get a very large number of long charged sidechains such as Arg, Lys etc on the surface.
I would like to manually adjust the reference energies for these residues in order to increase the penalty for these problematic residues. I assume this is possible but haven't been able to figure out which of parameters or weight files I need to change.
Can anyone help?
thanks a lot!
The reference energies are stored in the file rosetta_database/scoring/weights/standard.wts. If you're not using the standard scorefunction they'll be somewhere else in the same folder. The first line is "METHOD_WEIGHTS ref" and then 20 numbers - these are the 20 reference weights for the residues. They're in order by single letter code (ACDEFG...).
thank you very much for your help!
Has anyone in the Baker group or in the wider Rosetta community parameterized a set of weights specifically for surface residues redesign?
It would potentially be very helpful as I don't really like the surface residues you get when redesigning with the standard weights and suspect you'd get a lot of solubility problems - I often get a load of Phe, Tyr, and Trp stacking together on the surface.
Yes, someone is working on exactly this. He's in the middle of writing up a paper on it and hopes to release the weight sets soon - but the code and weights haven't been released yet.
You can use the POLAR command in resfiles at surface positions to restrict the residue set to only polar residues as a temporary solution?
that is excellent news - looking forward to seeing it!
I tried using POLAR and PIKAA etc but it still doesn't really solve the problem as you still get very odd surface residue compositions so that's why I wanted to adjust the ref energies manually.