AMBER Archive (2005)

Subject: Re: AMBER: difference of energy in sander and nmode in amber 7

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 17 2005 - 11:36:11 CDT

On Mon, Aug 15, 2005, sebnem wrote:

> I need to carry a molecule from nmode (amber 7), where i carried out NMA
> analysis, to sander(amber 7). However when I take the minimized structure
> from nmode, i am getting a different non-bonded energy term in sander.

>
> Here is the input of nmode:
> minimization,
> &data
> ntrun=4,
> cut=9999.0
> nprint=100,
> drms=0.00000001,
> maxcyc=2,
> scnb=2.0,
> scee=1.2,
> ibelly=1,
> idiel=1,
> &end
> group info
> RES 1 34
> END
> END

I think the belly option is implemented differently in nmode and in current
versions of sander. This means that some terms that would be fixed are
eliminated from nmode but not from sander.

Try to run without the belly option to see if this helps clear things up.

...good luck...dac

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