Dear All,
I am using MM PBSA (Amber10)...
as i was running the mm_pbsa.pl script for calculation of binding energy...i got errors like
Grid origin corrected at level 2 -21.750 3.375 3.750
PB bomb in pb_setgrd(): Allocation aborted 0 0 0
0 0 0 0 0 0
so i was advised by Dr. Ray Luo to sfix the fillratio to 2.0 and then
change the 'space' values from 0.75 to upwards with increments of 0.25
until the error disappears..(prior to this fillratio was 4.0)..
i followed his advice and ran the script with fillratio fixed at 2.0
and 'space' was varied from 0.75, then 1.0 then 1.25 the 1.5..
the errors were same for space values 0.75,1.0,1.25 but when space=1.5, the error was
"vertex atom mismatch
atom: 1291
vertex atom:1289"...
the output files for space values 0.75, 1.0, 1.25 &1.50 are pasted below...
1. when space = 0.75:
Grid dimension at level 1 71 55 71
Grid origin corrected at level 1 -73.500 -37.500 -48.750
Grid dimension at level 2 299 229
295
Grid origin corrected at level 2 -21.750 3.375 3.750
PB bomb in pb_setgrd(): Allocation aborted 0 0 0
0 0 0 0 0 0
0 0 0 0 0 0
0 0 0 0 0 0
0 0 0 0 41 0
0 0 0
2. when space = 1.0:
SA surface: setting up working radii
SA surface: found nonzero radii 3777
Number of SA srf points exposed455488
SA Bomb in sa_arc(): Allocation aborted 0 0 41
0 0
3. when space = 1.25:
Grid origin corrected at level 1 -125.625 -145.000 -102.500
Grid dimension at level 2 255 279 221
Grid origin corrected at level 2 -45.625 -62.500 -36.875
SA surface: setting up working radii
SA surface: found nonzero radii 3777
Number of SA srf points exposed820180
SA Bomb in sa_arc(): Allocation aborted 0 0 41
0 0
4. when space = 1.50:
FDPB Summary ========
Do FDPB every 1 steps
Nonbonded Update
residue cutoff is set to 12.000
fdpb cutoff is set to 5.000
sas cutoff is set to 9.000
nonbonded cutoff is set to 0.000
Grid Constants
Grid dimensions: 63 61 57
Grid spacing set to 6.000
Grid boundary
-156.750 221.250
-152.250 213.750
-126.750 215.250
Dielectric Map
Cavity radii in the prmtop file are used
Use probe-accessible surface definition
Compute SAS every 1 steps
Solvent probe radius: 1.400
Surface dots per atom 366
Buried atom radii increment 0.800
Threshhold for exposed atom 0.200
Current SAS ********
Boundary conditions
sum of grid charges as independent DH spheres
Physical constants
Solute dielectric constant : 1.000
Solvent dielectric constant : 80.000
Temperature (K) : 300.000
Ionic strength (mM) : 0.000
Debye-Huckel parameter (1/A): 0.000
FD Solver Option
Use Modified ICCG solver
Iteration data
Maximum iterations : 1000
Convergence criteria: 0.001
Iterations required : 38
Norm of the constant vector: 0.15507E+05
Norm of the residual vector: 0.15175E+02
Convergence achieved : 0.97860E-03
PB Warning in epsbnd(): No neighbor found for boundary grids
total: 87
Vikas Sharma (+91-9780449303)
Molecular Modeling lab.
Department of Medicinal Chemistry
National Institute of Pharmaceutical Education & Research (NIPER),
SAS Nagar, Mohali,
Punjab (INDIA)
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Received on Tue Jun 09 2009 - 01:16:59 PDT
