Hello,
I am attempting to predict the structure of a metalloenzyme after 5 mutations using the relax function. My current protocol consists of adding the following:
- Adding a mutation to the protein in pymol
- Relaxing the protein and picking the lowest energy structure
- Adding another mutation to the lowest energy structure and repeating until all mutations have been added.
Would this be the best protocol to perform this action or would it be better to just add all the mutations at once and then relax the protein? Also is there a better Rosetta program for doing this or for adding mutations? I have been getting good results but I was curious if there was a flaw in my protocol.
Thanks
Category:
Post Situation:
Your approach probably works ok, but might be unnecessarily complicated and computationally costly. You could introduce all mutations at once using the original structure as input and define the mutations in a resfile. With the flag `-packing:resfile path/to/resfile` you can input your resfile. In addition you should set `relax:respect_resfile true`.
If you are new to Rosetta you might also want to check out some packing options that are recommended in case you didn't set these already.
Example resfile: