I have been recently testing pH_protocol to calculate the pKa of one of my proteins. In the original paper, the authors include the weights function to be used with the protocol:
After replacing hack_elec to fa_elec everything works fine. However, while the results are mostly the same as the ones I get from running on ROSIE, a couple of sidechains get really different Pkas. Any ideas?
Here's the weights that the ROSIE server is using for the pKa protocol:
And here's the equivalent command that's being run:
Hopefully that will help you get started to debug the difference.
Also, keep in mind that Rosetta runs are typically stochastic. Multiple runs will result in slightly different values. How different depends on the system and the protocol. If the variation is small, it might just be a difference in run-to-run variability. I might suggest running the local runs several times to get a sense of the size of the stochastic variation.