Re: [AMBER] weired Ligand conformation during simulation

From: David A Case <>
Date: Sun, 31 Oct 2021 16:22:55 -0400

On Sun, Oct 31, 2021, Sadaf Rani wrote:

>I have observed the course of ligand during the whole trajectory and I
>observe that cofactor starts moving away from the binding site and this
>distance goes on increasing up to 15 angstroms and the adopts a
>conformation that changes its torsions very much. In case of the substrate,
>it falls far away from the protein. During the trajectory, I observed ring
>puckering and unusual torsion in terminal phosphate.

If the cofactor and substrate leave the binding pockets when they "should"
stay fixed, then there are many possible reasons for such behavior.
Generally, one would expect the torsions to change when a ligand leaves its
binding pocket. There may indeed be problems with the force field
description of your ligands, but it is certainly also possible that the
initial structure is not close enough to a conformation that is stable to
stay "put".

"Fixing" the problem is not something that can be done via email. You might
look quite carefully at the very beginning of the simulation: are the
cofactor or substrate changing their initial positions and conformations
right away? Can you find evidence of bad contacts that might be driving
this? How well do you know what the physically correct behavior is supposed
to be?

....good luck....dac

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Received on Sun Oct 31 2021 - 13:30:02 PDT
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