AMBER Archive (2009)

Subject: RE: [AMBER] QM/MM

From: Syed Tarique Moin (
Date: Wed May 06 2009 - 02:12:17 CDT

Thanks a lot.

Syed Tarique Moin,

Junior Research Fellow,

H.E.J. Research Institute of Chemistry,

International Center for Chemical and Biological Sciences,

University of Karachi, Karachi-75720, Pakistan

--- On Tue, 5/5/09, Ross Walker <> wrote:

From: Ross Walker <>
Subject: RE: [AMBER] QM/MM
To: "'AMBER Mailing List'" <>
Date: Tuesday, May 5, 2009, 3:16 PM

Hi Syed,

> But I m treating only one aminoacid that is alanine as in the QM/MM
> tutorial i.e NMA. In tutorial the same thing is happening i did the
> same thing i.e. same type of solvation and same input except the theory
> that is I used AM1.
> Alanine and NMA have about same number of atoms 11 and 12 atoms. I am
> not incorporating the water as in NMA QM/MM tutorials.

You still probably add more water. The Tutorial example is right on the
bleeding edge for having the smallest water box possible. Try upping your
solvatebox buffer by 1 angstrom or so.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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