AMBER Archive (2009)
Subject: Re: [AMBER] MM - PBSA problem
From: musa özboyacı (musaozboyaci_at_gmail.com)
Date: Mon Jan 26 2009 - 10:32:40 CST
I appreciate your helps and thanks a lot! There is another mail which is
about deleting these lines as well! I guess so that this might be the
source of the problem.
All the best,
2009/1/26 Cenk (Jenk) Andac <cenk_andac_at_yahoo.com>
> Hi Musa,
> Your files work fine at TR-GRID.
> However, I looked at file $AMBERHOME/src/mmpbsa/mm_pbsa_statistics.pm
> at TR-GRID and I noticed that I commented out lines 132, 133 and 137 as
> 132 # "ELRAELE" => [1,0,'ELRAELE = +(-?\d+\.\d+)'],
> 133 # "EPB" => [1,0,'EPB = +(-?\d+\.\d+)'],
> 137 # "PBNONPOL" => [1,0,'ENPOLAR = +(\d+\.\d+)'],
> I think this is how I got MMPBSA working at TR-GRID in the past. I am not
> really sure though if lines 132,133 and 137 are essential parts of the PB
> section. Nevertheless, you don't need these lines for the @PB parameters in
> binding_energy.mmpbsa file you sent. Please somebody corrects me if I am
> mistaken here.
> I also cross-checked your outputs using $AMBERHOME/src/mmpbsa/
> mm_pbsa_statistics.pm from AMBERv9 and I exactly got the same result as
> compared to that of MMPBSAv10 (with the modifications suggested above).
AMBER mailing list