AMBER Archive (2009)

Subject: RE: [AMBER] QM/MM

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue May 05 2009 - 17:16:26 CDT


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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|\oss Walker

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| San Diego Supercomputer Center |
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