AMBER Archive (2006)

Subject: Re: AMBER: hessian calculation

From: sebnem_at_mercury.chem.pitt.edu
Date: Wed Mar 29 2006 - 15:48:38 CST

Hi again,
I am trying to analyze the problem with a smaller system.
I think when i use icons option in nmode, in the second derivative
calculation part, it uses the restraints on the whole molecule not only
on the group that I define in the input file. Is this the way how
restraints are implemented in nmode?
thanks a lot,
sebnem

On Tue, 28 Mar 2006, David A. Case wrote:

> On Tue, Mar 28, 2006, sebnem_at_mercury.chem.pitt.edu wrote:
>
> > group
> > 1
> > RES 35 279
> > END
> > END
>
> I don't see anything obviously wrong, but this is a very big system to be
> doing normal modes on. If you want to explore things in more detail, try
> printing out the Hessian elements for a very small test case, and work your
> way up in size.
>
> ...dac
>
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