Re: [AMBER] Advice on applying restraints

From: David A Case via AMBER <>
Date: Mon, 18 Jul 2022 08:20:45 -0400

On Sat, Jul 16, 2022, Matthew Guberman-Pfeffer via AMBER wrote:
>Background: I have a disordered protein with a missing loop. I added
>the loop, and it connects well to the rest of the protein after
>minimization. But, between the added loop and the rest of the protein there
>is a “pore” and I’m not sure if the loop should be packed into that pore. I
>want to see if I can at least close the gap somewhat.

Generating models for missing loops in proteins is not something that Amber
is very good at. *Refining* these loops after initial coordinates are
available is something that often works. You can see some examples here:

   Systematic comparison of Amber and Rosetta energy functions for protein
   structure evaluation. J. Chem. Theory Comput. 14, 6015-6025 (2018).

This study used Rosetta to generate the initial candidate models, but other
tools to do this are also available. Note that you probably want to
generate a significant number of initial structures, then choose good ones
from such an ensemble.

...hope this helps....dac

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Received on Thu Aug 04 2022 - 13:34:33 PDT
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