Re: [AMBER] Ligand entry and exit path

From: Vlad Cojocaru <>
Date: Mon, 22 Jun 2015 17:55:34 +0200

Dear Debodyuti,

Maybe you'd like to take a look at the Random Accelerated Molecular
Dynamics Simulation method. Unfortunately although RAMD used to be
written for AMBER, this is not supported anymore. Instead RAMD can be
run in NAMD.

The RMAD tcl scripts are available with the NAMD distribution but can
also be downloaded here:

If you decide to run RAMD in NAMD with AMBER force fields, this page is
a "must view" before doing any simulations:

For references regarding the use of RAMD, please check the original
papers from Rebecca Wade's group ... You could also start with Cojocaru
et al. (2012) in Current Drug Metabolism and references therein.

Best wishes

On 06/22/2015 05:26 PM, Debodyuti Dutta wrote:
> Dear AMBER users,
> I want to investigate ligand entry path to the active site of a big protein
> and product exit pathways from the active site. Can someone please suggest
> me what type of analyses can be done in AMBER to serve this purpose. AMD
> or
> steered MD as described in the tutorials, do not seem proper for these kind
> of jobs.
> Thanks in advance.
> *Debodyuti Dutta*
> Research Scholar
> Indian Institute of Technology Kharagpur
> _______________________________________________
> AMBER mailing list

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
AMBER mailing list
Received on Mon Jun 22 2015 - 09:00:03 PDT
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