AMBER Archive (2008)

Subject: Re: AMBER: Help with NMODE

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Fri May 02 2008 - 11:50:35 CDT

Dear David,

Thanks for the quick reply.

On Fri, May 2, 2008 at 12:23 PM, David A. Case <case_at_scripps.edu> wrote:

> 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.
>

Yes, I am getting a different energy in my first step of nmode than my last
step of sander min. All of the terms are the same except for the
Electrostatics term.

> > 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.

My system is a double stranded DNA 10mer with 3 proflavine intercalators.
The DNA is decribed by parm94 with parmbsc0 improvements where as the
proflavines are described by the gaff ff. I am running Amber 8 with the
lastest bug fixes on an AMD 64, Redhat Enterprise 4. I generated 200
snapshots of an MD trajectory. Each snapshot is of the DNA-proflavine atoms
only (712 atoms total). I don't believe it is a problem with my prmtop file
because I'm able to run the script mmpbsa.pl to calculate GBSA / PBSA and MM
energies without any problems.

>
>
> 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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Thank you for your help,

Seth

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