AMBER Archive (2008)

Subject: Re: AMBER: problem with distance restrain

From: David A. Case (case_at_scripps.edu)
Date: Tue Mar 18 2008 - 14:00:11 CDT

On Tue, Mar 18, 2008, aneesh cna wrote:
>
> I am using version 9.0 of Amber . I am trying to put distance restrain in my
> system. During the fist minimization run got the following error in the
> output file even though minimization went fine.

The minimization did not go "fine", as the "not-a-numbers" attest.

>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 500 NaN NaN 0.0000E+00 F2 1

You should restart, doing a few steps (say 10-20) of minimization, with
ntpr=1, and study the output carefully. You can leave the restraints off
of this step, which might help narrow down where the problem is.

...dac

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