VMD-L Mailing List

From: Armen Nalian (nalianarmen_at_sfasu.edu)
Date: Wed Feb 16 2005 - 18:58:54 CST

Dear all,
I tried to run apbs and got this error message by the end of the run.
I am using dcd structure and .psf file as input.
Thank you,

Got PQR paths for 1 molecules
Reading PQR-format atom data from /tmp/ionized.pqr.
  41504 atoms
  Centered at (-1.700e-02, 1.550e-02, -5.000e-02)
  Net charge 3.99e-16 e
Preparing to run 2 PBE calculations.
----------------------------------------
CALCULATION #1: MULTIGRID
  Setting up problem...
  Vpbe_ctor: Using max ion radius (2 A) for exclusion function
  Debye length: 7.8566 A
  Current memory usage: 444.068 MB total, 444.068 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 129 x 129 x 129
  Grid spacings: 1.005 x 0.745 x 0.925
  Grid lengths: 128.630 x 95.412 x 118.432
  Grid center: (-0.017, 0.016, -0.050)
  Multigrid levels: 6
  Molecule ID: 1
  Linearized traditional PBE
  Single Debye-Huckel sphere boundary conditions
  2 ion species (0.150 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.150 M concentration
    2.000 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 1.000
  Solvent dielectric: 78.540
  Using "molecular" surface definition; harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature: 298.150 K
  Surface tension: 0.105 kJ/mol/A^2
  Solving PDE (see io.mc* for details)...
----------------------------------------
CALCULATION #2: MULTIGRID
  Setting up problem...
  Vpbe_ctor: Using max ion radius (2 A) for exclusion function
  Debye length: 7.8566 A
  Current memory usage: 439.920 MB total, 531.934 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 129 x 129 x 129
  Grid spacings: 0.670 x 0.497 x 0.617
  Grid lengths: 85.753 x 63.608 x 78.954
  Grid center: (-0.017, 0.016, -0.050)
  Multigrid levels: 6
  Molecule ID: 1
  Linearized traditional PBE
  Boundary conditions from focusing
  2 ion species (0.150 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.150 M concentration
    2.000 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 1.000
  Solvent dielectric: 78.540
  Using "molecular" surface definition; harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature: 298.150 K
  Surface tension: 0.105 kJ/mol/A^2
  Potential to be written to pot.dx
  Solving PDE (see io.mc* for details)...
  Writing potential to pot.dx
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage: 0.000 MB total, 531.934 MB high water

Thanks for using APBS!

apbsrun: error occurred while running APBS:
  parsePBE: Warning -- parsed deprecated "bcfl 1" statement
parsePBE: Please use "bcfl sdh" instead.
parsePBE: Warning -- parsed deprecated "srfm 1" statement.
parsePBE: Please use "srfm smol" instead.
NOsh: Warning -- parsed deprecated statment "chgm 1".
NOsh: Please use "chgm spl2" instead!
parsePBE: Warning -- parsed deprecated "calcenergy 0" statement.
parsePBE: Please use "calcenergy no" instead.
parsePBE: Warning -- parsed deprecated "calcforce 0" statement.
parsePBE: Please use "calcforce no" instead.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.