Re: AMBER: Minimization in sander and nmode

From: David A. Case <>
Date: Thu, 6 Oct 2005 03:06:33 -0700

On Thu, Sep 29, 2005, Mingfeng Yang wrote:
> At first, I managed to minimize the structure with sander to
> DRMS=9.5777E-05. Then, I tried to do NMA on the minimized strucutre with
> nmode, however, nmode complain the rms of step length (1.5) is larger
> than the drms value (0.0001).

It looks like you did the minimization in sander a regular dielectric model,
but then used an r**2 dielectric (idiel=0) in nmode. Make sure that you get
the same energies in both programs; otherwise you will see what you report.

....good luck...dac

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Received on Thu Oct 06 2005 - 11:53:00 PDT
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