Re: [AMBER] weired Ligand conformation during simulation

From: Sadaf Rani <>
Date: Sun, 31 Oct 2021 23:38:09 +0500

Dear Dr. David
Thank you very much for your reply.
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.
The screenshots are just to describe the ligands at the first and last
frame of trajectory.
Could you please help to fix this problem?
Thanks in advance.

On Sat, 30 Oct 2021 at 18:07, David A Case <> wrote:

> 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.
> ....dac
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Received on Sun Oct 31 2021 - 12:00:02 PDT
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