Syed Tarique Moin,
--- On Tue, 5/5/09, Ross Walker <ross.rosswalker.co.uk> wrote:
From: Ross Walker <ross.rosswalker.co.uk>
Subject: RE: [AMBER] QM/MM
To: "'AMBER Mailing List'" <amber.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
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Received on Wed May 20 2009 - 14:50:34 PDT
