Re: [AMBER] weired Ligand conformation during simulation

From: David A Case <>
Date: Sat, 30 Oct 2021 09:06:45 -0400

On Sat, Oct 30, 2021, Sadaf Rani wrote:

>I am working on a protein-ligand system for which I run 100 ns of
>simulation. On visual inspection I have observed that ligand adopts
>unexpected conformations and as shown in pdb structures. I have used RESP
>charges and antechamber for calculation of parameters.
>Could you please help me to figure out the source of the problem.

Are you sure this is really a "problem"? Finding unexpected ligand
conformations is one common goal in running MD simulations. It's not clear
(to me, at least) from just looking at the ligand snapshots, whether or not
something is wrong. You should examine the protein-ligand contacts, and
visualize the pathway going from early snapshot to the later one; that might
provide key information about what is driving the change.


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Received on Sat Oct 30 2021 - 06:30:02 PDT
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