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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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calculating non-protein electrostatics #511

Closed dvdvbrn closed 4 years ago

dvdvbrn commented 6 years ago

Hello everyone,

I don't think this issue with APBS, but rather with me and my input files. If there is more preferred resource for this type of questions please redirect me there, as of now I will ask it here...

I am trying to calculate electrostatic potential of nylon crystal with APBS, but the calculation is being killed with this kind of output:

======================================= This executable compiled on Oct 17 2016 at 16:11:10

Parsing input file 20180410_apbs-input.in... rank 0 size 1... read Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from 20180409_nylon-crystal-PDB2PQR-processed.pqr. 9999 atoms Centered at (5.393e+01, 7.398e+01, 8.006e+00) Net charge -1.25e+00 e Preparing to run 2 PBE calculations.

CALCULATION #1: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 12755.955 MB total, 12755.955 MB high water Using cubic spline charge discretization. Grid dimensions: 321 x 545 x 289 Grid spacings: 0.785 x 0.788 x 0.746 Grid lengths: 251.185 x 428.679 x 214.751 Grid center: (53.928, 73.984, 8.006) 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: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.134353099376E+05 kJ/mol Calculating forces...

CALCULATION #2: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Killed

Is this because my system is too big? Any help would be appreciated!!!

Thanks,

Vitali Stanevich Process Development Scientist, Janssen Pharmaceuticals

kozlac commented 6 years ago

Hello @dvdvbrn , it may be memory related since at the end of calculation one the memory usage is about 13gigs. What are your system specs? If you can share your .in, the io.mc created after running APBS, and .pqr files I could make sure nothing else is going on. If so, please send them to juan.brandi-lozano@pnnl.gov. Thanks!!