AMBER Archive (2009)

Subject: RE: [AMBER] QM/MM

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
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

tarisyed_at_yahoo.com

tarisyed_at_hotmail.com

--- On Tue, 5/5/09, Ross Walker <ross_at_rosswalker.co.uk> wrote:

From: Ross Walker <ross_at_rosswalker.co.uk>
Subject: RE: [AMBER] QM/MM
To: "'AMBER Mailing List'" <amber_at_ambermd.org>
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
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues. 

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber