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

From: Matias Machado <>
Date: Sat, 08 May 2021 15:15:29 -0300 (UYT)

Dear Tucker,

I faced the exact same issue while simulating an virus particle (See "Simulation details" in

Fortunately, I identified a missing lysine in the structure, which was reconstructed as a tryptophan ring piercing by Leap.

Contrary to expectations, minimization didn't push out the lysine side chain away, but increased its bonds up to a ridiculous length... and the MD didn't crush!

As Carlos mentioned in several mails, leap is not meant for model building and there are no fixes for that, so you have to find better ways to do it... :-/

Best regards,


Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Tucker Burgin" <>
Enviados: Viernes, 7 de Mayo 2021 12:36:52
Asunto: [AMBER] Avoiding steric snafus with protein mutations in tleap?

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 Sat May 08 2021 - 11:30:02 PDT
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