AMBER Archive (2009)

Subject: RE: [AMBER] QM/MM

From: Syed Tarique Moin (
Date: Mon May 04 2009 - 17:13:22 CDT


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.

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 Mon, 5/4/09, Ross Walker <> wrote:

From: Ross Walker <>
Subject: RE: [AMBER] QM/MM
To: "'AMBER Mailing List'" <>
Date: Monday, May 4, 2009, 10:47 AM

Hi Syed,

> I am simulating the aminoacid in water of 15 Angstrom layer using QM/MM
> implemented in amber10 using AM1 theory, but i am getting the following
> error, QM-Cutoff is larger than a box and you require a larger box.

This is saying that the size of the QM region + the cutoff would extend
beyond the edges of the box. The net result of this is that the system would
see its own images in the direct space sum which is not permitted.
Essentially this means that either your qmcut is too large (8 to 10
angstroms is probably good) and or your water box (QM+MM) is too small.

You should note though that if you are including water in the QM region it
will diffuse during the simulation into the MM water and this will
ultimately result in the calculation failing with the above error since the
effective size of your QM region will have grown as the water diffuses. I
have been developing approaches to deal with the issue of including mobile
waters in the QM region but this will not be ready until the next version of
AMBER is released.

Good luck,

|\oss Walker

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