AMBER Archive (2008)

Subject: Re: AMBER: Help with NMODE

From: David A. Case (case_at_scripps.edu)
Date: Fri May 02 2008 - 11:23:34 CDT

On Fri, May 02, 2008, Seth Lilavivat wrote:
>
> I am new to nmode and am having a few problems. I searched the archives and
> found my problem to be common but did not find a resolution. First, I am
> getting the "Root-mean-square gradient of input coords is" greater than the
> maximum that I requested error. I've changed "scee = 1.2" and bumped up
> MAXCYC as well.... no luck.

Did you minimize to a very low gradient in sander first? Are you getting a
different energy in nmode (on the first step) than on the last step of the
sander minimization.

> I am also getting a "DIHEDRAL ANGLE ERROR." As an example I've pasted the
> last part of my nmode.rec.1.out file:
>
>
> DIHEDRAL ANGLE ERROR: 10441788179118001803

This should have been a fatal error, but the code actually continues when it
should not. This means that somehow, nmode is not reading or interpreting
your prmtop file correctly, or memory is corrupted, or something. I don't
recall ever seeing this error reported before, so don't have much idea of what
could have caused it. We will need to know lots more about your system in
order to begin tracking this one down.

Also, we are encouraging people who can to use NAB rather than
nmode to compute normal modes now. (NAB is a part of AmberTools:
http://ambermd.org/#AmberTools). NAB has a bit of a learning curve, to be
sure, and we still want to keep nmode working.

...regards...dac

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