AMBER Archive (2008)

Subject: RE: AMBER: mm_pbsa error : Scale paremeter for PBSA

From: Ray Luo (
Date: Fri Sep 05 2008 - 12:45:12 CDT

We usually set fillratio to 2 or less for proteins and to 4 or larger for
small molecules. The SCALE controls the resolution of the finite-difference
grid, so usually we do not change it. The default SCALE = 2 1/A or space =
0.5 A is good if you can use it. If you don't have enough memory, you'll
have to reduce SCALE or increase space . to use a smaller finite-difference


All the best,



Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email:
Phones: (949) 824-9528, 9562


-----Original Message-----
From: [] On Behalf Of
Sent: Friday, September 05, 2008 10:27 AM
Subject: AMBER: mm_pbsa error : Scale paremeter for PBSA


Dear All,

The MM-PBSA utility program to calculate the binding energy stopped with an
error at one snapshot from the ligand set :
pbsa -O -i -o pbsa_lig.1.out -c ./GenerateSnapshots/md12_lig.crd.1
-p ./lig.prmtop not successful

The PBSA calculation failed for this snapshoT and tailing pbsa_lig.1.out
file shows :

 Ymin, Ymax, Ymax-Ymin: -12.492 5.055 17.547
 Zmin, Zmax, Zmax-Zmin: -8.579 1.046 9.625
   beginning box center at level 1 -10.000 -4.000 -4.000
   beginning box center at level 2 -10.000 -4.000 -4.000
 Grid dimension at level 1 3 5 3
 Grid origin corrected at level 1 -26.000 -28.000 -20.000
 Grid dimension at level 2 17 27 19
 Grid origin corrected at level 2 -19.000 -18.000 -14.000
PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000

I increased the scale to 4 in mm-pbsa input file and it did work

my question is how to choose this parameter "Scale"

best wishes

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