AMBER Archive (2006)

Subject: Re: AMBER: Free-energy using MM-PBSA

From: Yongmei Pan (ypan2_at_uky.edu)
Date: Thu Oct 19 2006 - 08:20:07 CDT

You needn't. Just do the complex and extract the complex, receptor and ligand from trajectories. Please see the input file format in AMBER manual.

-----Original Message-----
From: mathew k varghese <mathew_kvarghese_at_yahoo.co.in>
To: amber_at_scripps.edu
Date: Thu, 19 Oct 2006 09:05:45 +0100 (BST)
Subject: AMBER: Free-energy using MM-PBSA

Dear AMBER users,

I have question about free energy calculation using
MM-PBSA. In the tutorial it is seen that we need three
different trajectories to use with mmpbsa. Is the use
of snapshots from the same trajectory of the complex
for complex, receptor and ligand is a valid
assumption?

If we are simulating the complex for 4ns, then is it
necessary to simulate the receptor and ligand also
for 4ns to use the mmpbsa approach?

/\/\athew

Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India

email mathew_kvarghese_at_yahoo.co.in

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Yongmei pan
College of pharmacy, University of Kentucky

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