AMBER Archive (2009)

Subject: RE: [AMBER] PBSA: PB bomb in pb_setgrd()

From: Ray Luo (rayhuangluo_at_gmail.com)
Date: Wed Jan 07 2009 - 12:24:15 CST

Larry,

To reduce the memory usage you can first try to set "fillratio" from 2.0 to
1.5 for the protein/protein-complex while keeping "space" the same.

If this setting still asks for too much memory, you can try a coarser
"space" of 0.75 or 1.0.

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of Larry Layne
Sent: Wednesday, January 07, 2009 7:34 AM
To: amber_at_ambermd.org
Subject: [AMBER] PBSA: PB bomb in pb_setgrd()

I received an error when trying run the mmpbsa program on my protein
complex. The output in the out file that showed an error gave me the "PB
bomb in pb_setgrd()" error. After looking at the archive, I found a remedy
(http://archive.ambermd.org/200408/0093.html) that suggested that I set my
space value to 0.5, to which it was already set. I attempted the second
suggestion, which was using single precision, but could not find the file,
or any similar files, with which I could comment out the suggested line. Is
there any other means I can overcome this error in amber 9? I've included
the error output file.

Thank you,
Larry

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