Re: [AMBER] Ligand movement in protein cavatiy

From: Aldo Segura <>
Date: Sun, 1 Jun 2014 20:34:56 -0700 (PDT)


I think you should try to use docking to get a protein-ligand complex. Then, you can use it for a MD simulation with Amber. Take a look at the tutorial 3 in the Amber website:



Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229


El Domingo, 1 de junio, 2014 22:21:54, Jurgens de Bruin <> escribió:

Hi All,

Firstly I am new to AMBER and MD of proteins. I have been working on
Homology Modeling and Docking for 2years now and would like to start using
AMBER for MD purposes.

I do hope someone can be of assistance, I would like to know if it would be
possible to track the movement of a ligand within a protein cavity using
AMBER and if so point me in the correct direction?

Thanks a lot.

Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
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Received on Sun Jun 01 2014 - 21:00:02 PDT
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