Re: [AMBER] software assistance

From: Jason Swails <>
Date: Tue, 28 Jun 2011 11:54:18 -0600

Hi Joe,

You can see the tutorials page at The Amber11 package has the molecular dynamics engines that most people use in their studies. You can do some basic MD using AmberTools by writing a NAB program (implicit solvent) or using mdgx (explicit solvent).

However, larger systems and longer simulations will benefit from the high performance amber MD engine or the wide array of options in sander.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
On Jun 28, 2011, at 7:05 AM, "Mr. Joseph S. Castle" <> wrote:
> My name is Joe Castle and I was pointed in the direction of your software for assistance in protein folding modeling for analysis of peptides of interest. I have been playing around with the AmberTools 1.5 software package and was having a lot of trouble with finding any tutorials that I could get working. What would be the best way to learn how to use this software package and what functionality would be gained by having the Amber 11 Suite along with the AmberTools 1.5
> Thanks
> Joe
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Received on Tue Jun 28 2011 - 11:00:06 PDT
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