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

From: Wei Huang <whuang.cct.lsu.edu>
Date: Tue, 10 Mar 2009 05:30:50 -0500

Hi Young,

Did you try fillratio = 4? It works for me when I had the same problem.

Best,
Wei

-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Zhu, Yong-Liang
Sent: Monday, March 09, 2009 11:31 PM
To: amber.ambermd.org
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 mm_pbsa.pl 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.

 

Young

 


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Received on Wed Mar 11 2009 - 01:22:24 PDT
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