[AMBER] Avoiding steric snafus with protein mutations in tleap?

From: Tucker Burgin <tburgin.uw.edu>
Date: Fri, 7 May 2021 11:36:52 -0400

Amber users,

I often use tleap to apply mutations to proteins by deleting the sidechain
of the residue I want to mutate and renaming it to the target residue name.

This usually works great, but every now and then the new sidechain atoms
that tleap adds will be inserted *through* a ring on another residue,
resulting in a badly unphysical state that can't be resolved with
minimization or equilibration simulations.

Usually I just fix such issues manually, but I have need to generate a
large number of mutants and can't manually check every structure. Are there
any scriptable tools within tleap (or other scriptable Amber tools like
pytraj or parmed) that can detect and/or fix these sorts of problems? I
don't need to get the "best" possible coordinates, I just need them to be
reasonable! tleap's "relax" command does not seem to be sufficient for this.

I know I could use something more suited to the purpose like Rosetta, but
it would be a lot more convenient if I didn't have to!

-Tucker Burgin
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Received on Fri May 07 2021 - 09:00:02 PDT
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