AMBER Archive (2009)

Subject: Re: [AMBER] NAB entropy calcualtion

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Fri Jan 09 2009 - 03:28:48 CST

Hi Ashok,
>
> I am working with a protein consisting of 6000 atoms and trying to
> calculate its entropy using NAB. Previously I had a memory issues and now
> we upgraded to 20GB of memory. However the run crashed producing the
> following output. It would be very helpful if someone could explain what
> the error means.
> Here is the output
> Reading parm file (asa.top)
...the rms gradient seems way too large for starting Newton-Raphson
minimization (and for obtaining thermodynamic quantities that make any
sense). I'd like to take a look ath the problem myself, but for that I'd
need prmtop, pdb and nab-source.

best,
Andreas

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