Re: Simulating a Binding Event

From: Lutimba Stuart (
Date: Tue Mar 06 2018 - 12:44:52 CST

Hej Alex,
I think to simulate the binding events of N-3-OXO-DODECANOYL-L-HOMOSERINE
LACTONE in your quorum sensing protein, you may concider the application of
Steered molecular dynamics *SMD of Targeted molecular dynamics to observe
the binding events as well as the free energy profiles from the simulation.
The link attached is a manual from NAMD that can held out.

Lutimba Stuart

On Tue, Mar 6, 2018 at 6:53 PM, Alex Saad-Falcon <>

> Hello All,
> I am fairly new to using NAMD and VMD for sophisticated simulations, but I
> was just wondering about the general process to simulate a binding event
> between a protein and a ligand. For example, I have this protein
> in which the pdb file includes the
> ligand (I believe). Do I need to move the ligand out of the protein but
> close to the binding site, and then run NAMD?
> Thanks for any feedback,
> Alex

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