RE: [AMBER] PB Bomb from MM-PBSA of Amber 10

From: Ray Luo <>
Date: Tue, 10 Mar 2009 09:28:15 -0700

What if you set it to 4? If it still doesn't work, please email me a sample
data set so I can reproduce your bug and find out why ...

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 Zhu, Yong-Liang
Sent: Monday, March 09, 2009 9:31 PM
Subject: [AMBER] PB Bomb from MM-PBSA of Amber 10

Hello there,


I used Amber 10 to simulate a small molecule bound in a protein. When I
used to calculate ligand-protein binding energy, the
calculation stopped when it calculated energy of ligand of frame 3. I
checked the file pbsa_lig.3.out and the file gave the following message
at the end:


PB Bomb in setgrd(): focusing grid too large 2

reset fillratio to a larger number 2.000


I understand that similar messages from old version of amber had been
discussed. In fact I set fillratio to 3 in the perl code based on those
discussions. But the issue remains.


Thank in advance.




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