Dear All,
The MM-PBSA utility program to calculate the binding energy stopped with an error at one snapshot from the ligand set :
pbsa -O -i pbsa.in -o pbsa_lig.1.out -c ./GenerateSnapshots/md12_lig.crd.1 -p ./lig.prmtop not successful
The PBSA calculation failed for this snapshoT and tailing pbsa_lig.1.out file shows :
Ymin, Ymax, Ymax-Ymin: -12.492 5.055 17.547
Zmin, Zmax, Zmax-Zmin: -8.579 1.046 9.625
beginning box center at level 1 -10.000 -4.000 -4.000
beginning box center at level 2 -10.000 -4.000 -4.000
Grid dimension at level 1 3 5 3
Grid origin corrected at level 1 -26.000 -28.000 -20.000
Grid dimension at level 2 17 27 19
Grid origin corrected at level 2 -19.000 -18.000 -14.000
PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000
I increased the scale to 4 in mm-pbsa input file and it did work
my question is how to choose this parameter "Scale"
best wishes
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Received on Sun Sep 07 2008 - 06:07:52 PDT
