AMBER Archive (2009)

Subject: [AMBER] NAB entropy calcualtion

From: chaitanya koppisetty (ashok_at_chalmers.se)
Date: Fri Jan 09 2009 - 03:01:13 CST

Dear List,

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)
title:

        mm_options: rgbmax=100.
        mm_options: cut=100.0
        mm_options: ntpr=50
        mm_options: nsnb=999
        mm_options: gb=1
        mm_options: diel=C
      iter Total bad vdW elect nonpolar genBorn
frms
ff: 0 -17363.99 6392.34 -3058.13 -12467.87 0.00 -8230.33
1.47e+00
ff: 50 -17780.88 6261.46 -3247.76 -12614.70 0.00 -8179.89
8.41e-01
        mm_options: ntpr=1
ff: 1 -17780.88 6261.46 -3247.76 -12614.70 0.00 -8179.89
8.41e-01
      iter Total bad vdW elect nonpolar genBorn
frms
ff: 1 -17780.88 6261.46 -3247.76 -12614.70 0.00 -8179.89
8.41e-01
 adding 0.00000 to diagonal of the hessian
rms of search direction: 0.8406775
For alpha = 0.00000 energy = -17780.8798943200
For alpha = 1.00000 energy = 5783104038003143.0000000000
For alpha = 0.66191 energy = 21606902961848412.0000000000
For alpha = 0.43929 energy = 444490269823.5280151367
For alpha = 0.28986 energy = 651934800.3937441111
For alpha = 0.38635 energy = 4186556325491628834816.0000000000
For alpha = 0.34101 energy = 241008358592.2326049805
For alpha = 0.32090 energy = 3458832486.3402562141
ff: 2 3458832486.34 1264939.95 3457590555.62 -12133.27 0.00
-10875.95 7.12e+08
asp: sff2.c:1266: ephi2: Assertion `bi > 0.01' failed.
Aborted

Regards,
Ashok.

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