Hi all,
I am attempting to predict the conformations of an enzyme after a single mutation. I have been using pymol to place the mutation into the protein and then I use the rosetta relax application to optimize the structure. Is this a valid way of performing this technique? Or should I be using rosetta scripts and repack the sidechains instead. I am worried that the relax protocol may not be able to optimize the residue if pymol puts it in a conformation that is far away from the optimal conformation.
Thank you!
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Relax does sidechain optimization, so as long as you're not limiting the sampling (e.g. by using the flags for sidechain constraints) the exact input conformation doesn't matter. So this approach would work. (As would simply editing the input PDB to change the residue three letter code -- when Rosetta reads in a PDB, it will add/remove atoms to make the residues what they should be for the particular designation.)