AMBER Archive (2005)

Subject: Re: AMBER: error in pbsa calculation

From: mingche Pan (panmingche_at_yahoo.com)
Date: Wed Apr 27 2005 - 11:20:10 CDT

Hi Ray,
 
Thanks for your answer! Yeah, it works now, but I have another problem. The pbsa calculation complained about " PB bomb in pb_reslist(): maxnbr too small". I modified the source code by increasing "cutres" from 11.0 to 15.0. Then it seems to fix the problem, but I am not sure whether the value I picked is reasonable.
 
Another question about pbsa calculation is what kind of discrepancy it would be for the GB and PB (both delphi and pbsa) calculation? In my case (just testing on several snapshots), the energy difference between this two methods is up to ~80 kcal/mol. There must be something wrong. Could you suggest me a few papers of on pbsa?
 
Thank you!
 
Mingche
Date: Tue, 26 Apr 2005 14:39:50 -0700
From: Ray Luo
Reply-To: amber_at_scripps.edu
To: amber_at_scripps.edu
Subject: Re: AMBER: error in pbsa calculation

>
> PB Bomb in setgrd(): focusing grid too large 2
> reset fillratio to a larger number 2.000
>
Please change fillratio to 4.0 instead of 2.0 in your input file as
instructed.

Ray

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