AMBER Archive (2009)

Subject: [AMBER] Vertex atom mismatch in Amber

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Wed Jun 10 2009 - 22:29:57 CDT

  
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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