Hi Davide,

Can you try sending the attachments again please? I ran into a similar case recently, but I am not sure if the solution works for you or not, unless I can take a look at the input files.

Thanks,

Yong


On Mon, May 18, 2009 at 6:39 PM, Davide Mercadante <dmer018@aucklanduni.ac.nz> wrote:
Dear APBS,

I tried to run apbs to compute the electrostatic grid on a pqr file of an oligosaccharide molecule (10mer). I created the pqr file using the pdb2pqr program and giving the ligand parameters specified in a mol2 file created with the dundee PRODRG Server. the pdb2pqr program also created the .in file for the apbs run. However, I got the following output.

Vpmg_fillco:    xmin = 8.339, xmax = 8.509
Vpmg_fillco:    ymin = -18.6305, ymax = -18.4605
Vpmg_fillco:    zmin = 0.8715, zmax = 1.0415
Vpmg_fillco:  Atom #202 at (21.637, -33.719, -9.182) is off the mesh (for cubic splines!!) (ignoring this atom):
Vpmg_fillco:    xmin = 8.339, xmax = 8.509
Vpmg_fillco:    ymin = -18.6305, ymax = -18.4605
Vpmg_fillco:    zmin = 0.8715, zmax = 1.0415
Vpmg_fillco:  Atom #203 at (21.267, -32.358, -7.380) is off the mesh (for cubic splines!!) (ignoring this atom):
Vpmg_fillco:    xmin = 8.339, xmax = 8.509
Vpmg_fillco:    ymin = -18.6305, ymax = -18.4605
Vpmg_fillco:    zmin = 0.8715, zmax = 1.0415
Vpmg_fillco:  Atom #204 at (20.980, -34.633, -5.634) is off the mesh (for cubic splines!!) (ignoring this atom):
Vpmg_fillco:    xmin = 8.339, xmax = 8.509
Vpmg_fillco:    ymin = -18.6305, ymax = -18.4605
Vpmg_fillco:    zmin = 0.8715, zmax = 1.0415
  Debye length:  0 A
  Current memory usage:  11.249 MB total, 15.429 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 33 x 33 x 33
  Grid spacings: 0.005 x 0.005 x 0.005
  Grid lengths: 0.170 x 0.170 x 0.170
  Grid center: (8.424, -18.546, 0.957)
  Multigrid levels: 4
  Molecule ID: 1
  Linearized traditional PBE
  Single Debye-Huckel sphere boundary conditions
  0 ion species (0.000 M ionic strength):
  Solute dielectric: 2.000
  Solvent dielectric: 2.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  298.150 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 0.000000000000E+00 kJ/mol
  Calculating forces...
----------------------------------------
CALCULATION #4: MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (0 A) for exclusion function
  Debye length:  0 A
  Current memory usage:  11.249 MB total, 15.429 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 33 x 33 x 33
  Grid spacings: 0.005 x 0.005 x 0.005
  Grid lengths: 0.170 x 0.170 x 0.170
  Grid center: (8.424, -18.546, 0.957)
  Multigrid levels: 4
  Molecule ID: 1
  Linearized traditional PBE
  Boundary conditions from focusing
  0 ion species (0.000 M ionic strength):
  Solute dielectric: 2.000
  Solvent dielectric: 2.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  298.150 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 0.000000000000E+00 kJ/mol
  Calculating forces...
----------------------------------------
PRINT STATEMENTS

print energy 2 - 1 end
  Local net energy (PE 0) = 0.000000000000E+00 kJ/mol
  Global net ELEC energy = 0.000000000000E+00 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage:  0.049 MB total, 15.429 MB high water


Thanks for using APBS!

I attach the file .pqr and .in of the molecules created using pdb2pqr.

Seems that all the atoms have been ignored and that the total energy is 0.0 Kj/mol
Please, can you help me to understand why this happens and how I can solve the problem?

Thanks infinitely in advance for you help.

All the Best,
Davide

Davide Mercadante
PhD Student - Department of Chemistry -
Rm 438 - telephone ext. 89171
Faculty of Science
The University of Auckland
Auckland, New Zealand


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--
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine