Dear Jenk,
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,
Musa
2009/1/26 Cenk (Jenk) Andac <cenk_andac.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
> follows.
>
> line
> 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).
>
> cheers,
>
> Jenk
>
>
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Received on Wed Jan 28 2009 - 01:11:15 PST
