Binding Energy

This cube calculates ligand binding energies using Zap TK.

Ligands are read from the intake port, and the protein is read from the init port.

The calculated energies are added to the intake port record and emitted through the success port.

Related Cubes

Calculation Parameters

  • Zap boundary spacing (boundary_spacing) type: decimal: Spacing between the molecule and the edge of the grid
    Default: 4.0 , Min: 1.0, Max: 10.0
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 192
  • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • Focus Target (focus_target) type: boolean: Flag if binding energy calculation should focus around ligand
    Default: False
  • GPUs (gpu_count) type: decimal: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Zap grid spacing (grid_spacing) type: decimal: Grid spacing for the internal Zap calculations
    Default: 0.75 , Min: 0.5, Max: 1.5
  • Inner dielectric (inner_dielec) type: decimal: Protein dielectric constant for Zap calculations
    Default: 1.0 , Max: 80.0
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Metric Period (metric_period) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Outer dielectric (outer_dielec) type: decimal: Solvent dielectric constant for Zap calculations
    Default: 80.0 , Max: 80.0
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required

Field parameters

  • Buried Area Energy Field (area_ene_field) type: Field Type: Float: Energy penalty associated with the buried area of the complex
    Default: Buried Area Energy
  • Buried Area Field (area_field) type: Field Type: Float: Buried area of the complex
    Default: Buried Area
  • Binding Energy Field (bind_ene_field) type: Field Type: Float: Protein ligand binding energy
    Default: Binding Energy
  • Coulomb Energy Field (coul_ene_field) type: Field Type: Float: Protein ligand Coulomb energy
    Default: Coulomb Energy
  • None (in_mol_field) type: Field Type: Chem.Mol:
  • Protein Field (init_mol_field) type: Field Type: Chem.Mol: Host protein molecule
  • None (out_mol_field) type: Field Type: Chem.Mol:
  • Zap Energy Field (zap_ene_field) type: Field Type: Float: Protein ligand Zap grid energy
    Default: Zap Energy

Hardware Parameters

Machine hardware requirements
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • GPUs (gpu_count) type: decimal: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 192
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters
  • Metric Period (None) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network

Parallel Binding Energy

The parallel version adds these extra parameters.

  • Number of messages to distribute at a time (item_count) type: integer: The maximum number of messages to bundle together for a parallel cube.
    Default: 1 , Min: 1, Max: 65535
  • Maximum Failures (max_failures) type: integer: The maximum number of times to attempt processing a work item
    Default: 10 , Min: 1, Max: 100
  • Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this Cube
    Default: 1000 , Min: 1
  • Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this Cube
    Default: 0
  • Starting number of Cubes (scaleup_start) type: integer: The initial number of concurrently running copies of this Cube
    Default: 2 , Min: 1