AMBER Archive (2008)

Subject: Re: AMBER: peptide MD

From: Gustavo Seabra (
Date: Mon Oct 27 2008 - 12:36:35 CDT

On Mon, Oct 27, 2008 at 1:13 PM, Beale, John wrote:
> On 10/27/08, Beale, John wrote:
>> I need to set up a system to use MD simulate the interaction of two
>> decameric peptides in explicit solvent. I need some guidance. Can I use
>> LEaP to set up such a system? How do I proceed?

> I have a PDB file, no constraints.

What's in that PDB file? Is it already with the 2 peptides, or one PDB
file for each?

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
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