AMBER Archive (2009)

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

From: Zhu, Yong-Liang (Yong-Liang.Zhu_at_elan.com)
Date: Tue Mar 10 2009 - 11:06:43 CDT

Hello Wei,

Thank you for your response. I did set fillratio=4 on line 435 of
mm_pbsa_createinput.pm. But I doesn't help - It seems nothing has
changed. Where did you set that value?

Young

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
Behalf Of Wei Huang
Sent: Tuesday, March 10, 2009 3:31 AM
To: 'AMBER Mailing List'
Subject: RE: [AMBER] PB Bomb from MM-PBSA of Amber 10

Hi Young,

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

Best,
Wei

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