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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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terminated by signal SIGSEGV (Address boundary error) #528

Closed amaurypm closed 4 years ago

amaurypm commented 4 years ago

Hello, I am trying to run apbs with a viral capsid (> 30,000 residues) and apbs crash. For example, the last lines of the output: ... Debye length: 7.8566 A Current memory usage: 34859.972 MB total, 34859.972 MB high water Using cubic spline charge discretization. Grid dimensions: 609 x 609 x 609 Grid spacings: 0.813 x 0.812 x 0.813 Grid lengths: 494.034 x 493.943 x 494.057 Grid center: (366.490, 141.841, 141.679) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 1.380 A-radius, 1.000 e-charge, 0.150 M concentration 1.810 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated

terminated by signal SIGSEGV (Address boundary error).

I have plenty of RAM, 126 GB, and apbs is not near this value before crashing.

kozlac commented 4 years ago

Hello @amaurypm ! Could you share your .in and pqr file to help reproduce and debug the problem?

amaurypm commented 4 years ago

Here they go.

model_AAV2.zip

sobolevnrm commented 4 years ago

The input file for this example was set up incorrectly: most of the atoms were off the mesh.