AMBER Archive (2009)

Subject: Re: [AMBER] NAB md function prints strange output

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Mar 12 2009 - 16:04:15 CDT

Hi,

Nor do I recall seeing this behavior.
As Dave suggested, send explicit and verbose details so that this
can be investigated.

thanks,
Scott

On Tue, 10 Feb 2009, David A. Case wrote:

> On Tue, Feb 10, 2009, Jochen Heil wrote:
>
> > I should have added one more thing. The system under investigation was a
> > complex of a protein and a general organic ligand, parameterized using
> > GAFF. The ambertools handbook says
> > "Force field calculations (e.g. molecular dynamics and minimization) can
> > be carried out with an implementation of the AMBER force field."
> > I assumed, this means all amber force-fields, including GAFF and GLYCAM.
> > Maybe this causes the "nan".
>
> Who knows? Unless you debug it yourself, or post an example that fails
> so that others can reproduce the problem, this is not going to get
> fixed.

On Mon, 9 Feb 2009, Jochen Heil wrote:

> i am trying to mimick the structure preparation of the score24 protocol
> of DOCK6 with NAB. The CG minimization seems to work as expected whereas
> the MD routine behaves strange. For some reason, i get "nan" for the
> total energy as well as the nonpolar part. Since i switched off GBSA, i
> would expect zero, but "nan" seems to point to a wrong setup or logical
> error, especially when printed in the total energy column. We have
> looked at the MD trajectory and found nothing suspicious, e.g. no
> clashes. Is this just NABs behaviour or is there an obvious problem with
> my settings?
>
> Input options are taken from the DOCK implementation:
> For CG: diel=C, gbsa=0, nsnb=99999, cut=18.0, gb=5
> For MD:diel=C, dt=0.001, gamma_ln=2, rattle=0, cut=18.0, gb=5,
> tempi=300.0, temp0=300.0, ntwx=10
...

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