Re: [AMBER] charting Ligand's movement in the binding pocket

From: Markowska <>
Date: Thu, 9 Jan 2020 21:02:08 +0100

Hi Prasanth!

If your protein of interests have a buried active site and/or you would
like to analyse the ligands' flow through a particular cavity, I would
recommend you a software developed by my research group, the AQUA-DUCT
In case you save the simulation frames after each picosecond (for longer
simulations, more than 100 ns, after 5 ps), AQUA-DUCT will provide you
pathways of each ligand's molecule, enable clustering the ligands on the
protein's surface and give you detailed statistics on, for example which
way do the ligands enter the binding pocket, how fast are they moving, how
long are they staying inside the cavity etc.
If you're interested, please check the AQUA-DUCT website:
We have recently added some new features and published another AQUA-DUCT
paper. It's a quite powerful, but still not so popular tool for analysis of
MD simulations.
I hope, it will be helpful in your case!

Best regards,
Karolina Mitusińska

czw., 9 sty 2020 o 11:55 Prasanth G, Research Scholar <> napisał(a):

> Dear All,
> I am interested in charting the trajectory of the ligand with respect to
> the residues of the binding pocket, during the simulation.
> May be representing the center of mass of the ligand as a dot at each
> frame, would help us see the path traced by the ligand in the pocket,
> during the simulation. Is there a possibility to do this during the
> trajectory analysis period / post production..?
> I was wondering if we could perform PCA and impose the ligand's trajectory
> on the bound complex and visualize only the ligand's movement with respect
> to the amino acid residues of the binding pocket. But this would not give a
> clear idea as the residues in binding pocket also move during the course of
> simulation.
> Hoping that i was able to explain it well enough..
> Thank you in advance.
> --
> Regards,
> Prasanth.
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Received on Thu Jan 09 2020 - 12:30:02 PST
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