Re: [AMBER] Tracking ligand position throughout equilibration stages

From: Dr. Anselm Horn <>
Date: Mon, 13 Jan 2020 10:34:40 +0100

Hi Debarati,

another possibility to monitor the movements of the ligand within its
binding pocket with a single variable is to rms-fit the trajetory to the
initial receptor structure and then calculate the rmsd value of the
ligand without fitting/superimposition. Thus, you obtain an rmsd vs.
time plot describing the flexibility of the ligand with respect to its
initial structure with respect to the protein environment.

However, since you imposed harmonic restraints upon your ligand, you
probably won't see large movements.

Hope that helps.



On 01/11/2020 04:21 PM, Debarati DasGupta wrote:
> Dear users,
> I have a naive question regarding tracking my ligand position as the trajectory progresses (5ns of equilibration); I have a weak ligand tethered to a binding pocket of a receptor and have applied restraint=20 throughout the minimization and equilibration steps so that it does not move out of the pocket.
> But I was wondering would I be able to use cpptraj (any action commands) to track how much the ligand actually moves throughout my 5ns of NPT equilibration.
> Is there a way to do it?
> I can write a distance script and try to find the distance of the ligand to the center of the binding pocket per frame (using cpptraj distance command), but I thought there may be another way to do it?
> Thanks
> Debarati
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Received on Mon Jan 13 2020 - 02:00:02 PST
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