AMBER Archive (2009)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Feb 10 2009 - 06:46:40 CST

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.

..dac

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