AMBER Archive (2009)

Subject: Re: AMBER: Re: nmode error: bad nonbon (amber 10)

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Jan 06 2009 - 08:32:48 CST

On Tue, Jan 06, 2009, Jeremy Harris wrote:
>
> I'm trying to do a NMA for a 170 residue long protein,
> step = 0
> F = -0.117597E+04 GRDMAX = 0.124782E+03 GNORM = 0.182217E+02

As I stated in my earlier email, the large value of GNORM here suggests
that the energies you are getting in sander are not equal to those in
nmode. Check the components carefully. The most likely problem is that
the default value for scee is *not* the same in nmode as it is in
sander.

...dac

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