AMBER Archive (2007)

Subject: AMBER: help in QM/MM simulation

From: Pankaj R. Daga (pdaga_at_olemiss.edu)
Date: Thu Dec 13 2007 - 15:02:17 CST

Dear Amber Community

 

I have a very stupid question. I want to perform QM/MM simulation on one
protein-ligand system. The system, I have been dealing with, needs water
molecules for the reaction chemistry in the active site. I have been
considering three different approaches for the same.

 

 

1. Minimize and equilibrate the system with MM and then directly start
with QM/MM production run

2. Minimize with MM and further processing with QM/MM potentials.

3. Start QM/MM processing directly from beginning.

 

Although, Approach-3 looks to be very convenient, at early stage it is very
difficult to pin-point the water molecules, to be included in QM region.

 

I am very new to QM/MM simulation. I would be grateful to you if you could
suggest me the right approach.

 

Regards

 

Pankaj

 

===============================================================
If your ship doesn't come in, swim out to it...Jonathan Winters
===============================================================
Pankaj R. Daga |
Department of Med. Chemistry | e-mail: pdaga_at_olemiss.edu
417 Faser Hall, | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
===============================================================

 

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