AMBER Archive (2008)

Subject: RE: AMBER: peptide MD

From: Beale, John (jbeale_at_stlcop.edu)
Date: Mon Oct 27 2008 - 12:47:42 CDT

One PDB file for each.

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Gustavo Seabra
Sent: Monday, October 27, 2008 12:37 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: peptide MD

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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