Dear All
I am trying to calculate the binding energy of ligand-receptor complex and I mutated one of the residues to ALA, after extracting the coordinates of ligand, receptor and complex, I tried to run the $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log, after that the program stopped suddenly while it was calculating the energy of ligand. I checked everything related to files.
Here is the file of pbsa_lig.1.out:
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4. RESULTS
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NB-update: residue-based nb list 3771
NB-update: atom-based nb list 2847
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 72.000 57.000 42.000
Xmin, Xmax, Xmax-Xmin: 66.637 76.401 9.764
Ymin, Ymax, Ymax-Ymin: 50.230 63.667 13.437
Zmin, Zmax, Zmax-Zmin: 29.381 53.914 24.533
beginning box center at level 1 72.000 57.000 42.000
beginning box center at level 2 72.000 57.000 42.000
Grid dimension at level 1 3 5 7
Grid origin corrected at level 1 56.000 33.000 10.000
Grid dimension at level 2 19 21 33
Grid origin corrected at level 2 62.000 46.000 25.000
PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000
What canI do in this regard!
Any help would be highly appreciated.
Cheers,
Maryam
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Received on Sun Dec 19 2010 - 03:30:03 PST
