AMBER: help in QM/MM simulation

From: Pankaj R. Daga <>
Date: Thu, 13 Dec 2007 15:02:17 -0600

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.






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


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Received on Sun Dec 16 2007 - 06:07:22 PST
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