Does anyone know how to fix it? Or what is the problem I'm having? I'm a newbie.
I'm getting the following message when I try to use POVME with small grid spacings and large radii:
numpy.core._exceptions._ArrayMemoryError: unable to allocate 9 GiB for an array with shape (37910, 37910) and data type float64
See a sample of the script below:
Parameters:
GridSpacing: 0.4
PointsIncludeRegions: sphere at (5.912, 2.767, 17.236), radius = 14.0
SavePoints: True
PDBFileName: protein-final.pdb
DistanceCutoff: 1.09
ConvexHullExclusion: True
ContiguousPocketSeedRegions: sphere at (5.912, 2.767, 17.236), radius = 4.0
ContiguousPointsCriteria: 3
NumProcessors: 4
UseDiskNotMemory: False
OutputFilenamePrefix: pov04/POVME_
SaveIndividualPocketVolumes: True
SavePocketVolumesTrajectory: False
OutputEqualNumPointsPerFrame: False
SaveTabbedVolumeFile: True
SaveVolumetricDensityMap: False
CompressOutput: False
Does anyone know how to fix it? Or what is the problem I'm having? I'm a newbie.
I'm getting the following message when I try to use POVME with small grid spacings and large radii:
numpy.core._exceptions._ArrayMemoryError: unable to allocate 9 GiB for an array with shape (37910, 37910) and data type float64
See a sample of the script below:
Parameters:
GridSpacing: 0.4
PointsIncludeRegions: sphere at (5.912, 2.767, 17.236), radius = 14.0
SavePoints: True
PDBFileName: protein-final.pdb
DistanceCutoff: 1.09
ConvexHullExclusion: True
ContiguousPocketSeedRegions: sphere at (5.912, 2.767, 17.236), radius = 4.0
ContiguousPointsCriteria: 3
NumProcessors: 4
UseDiskNotMemory: False
OutputFilenamePrefix: pov04/POVME_
SaveIndividualPocketVolumes: True
SavePocketVolumesTrajectory: False
OutputEqualNumPointsPerFrame: False
SaveTabbedVolumeFile: True
SaveVolumetricDensityMap: False
CompressOutput: False