Gameplan

This cube analyzes a protein and a bound or docked ligand to determine points where solvent information may be interesting, runs szmap at these points, and then processes the results, formulating various hypotheses for ligand modification and identifying sites where water is stabilizing or destabilizing.

Related Cubes

Calculation Parameters

  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • 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
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • 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
  • Max Rotors (max_rotors) type: integer: Cutoff of rotatable bonds. The cube will skip molecules with rotors more than the cutoff.
    Default: 40 , Min: 1, Max: 9999
  • 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
  • Merge Distance (merge_dist) type: decimal: Maximum distance (in Angstroms) for merging 2 sample points.
    Default: 0.35 , Max: 2.0
  • 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
  • Missing Hydrogen Ok (missing_h_ok) type: boolean: If specified, missing hydrogen’s will not lead to calculation failure. Otherwise, missing hydrogen’s on the ligand or on more than 10 percent of the protein heavy atoms will cause calculation to fail.
    Default: False
  • Number Orientations (num_orients) type: integer: The maximum number of orientations for the SZMAP probe.
    Default: 60 , Min: 2, Max: 9999
  • 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
  • Sample sp3 hybridization (sp3_aromatic) type: boolean: Sample sp3 hybridization at each aromatic ligand atom.
    Default: False
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Water Stabilization (stable_water) type: boolean: Search for regions where water is stabilized or destabilized by in the protein/ligand complex.
    Default: True

Field parameters

  • Depiction Molecule (depict_mol_field) type: Field Type: Chem.Mol: Output molecule field for Gameplan depiction.
    Default: Depiction Molecule
  • ES Energy field (es_energy_field) type: Field Type: Float: ES Free Energy
    Default: ES Energy
  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • Hypothesis Type field (hypothesis_field) type: Field Type: String: Hypothesis type
    Default: Hypothesis Type
  • Input Ligand (in_mol_field) type: Field Type: Chem.Mol:
  • Input Protein (in_protein_field) type: Field Type: Chem.Mol:
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • None (out_mol_field) type: Field Type: Chem.Mol: Output molecule field for Gameplan results.
  • Stabilizing Energy field (stable_ene_field) type: Field Type: Float: Stabilizing Energy
    Default: Stabilizing Energy
  • Destabilizing Energy field (unstable_ene_field) type: Field Type: Float: Destabilizing Energy
    Default: Destabilizing Energy
  • VdW Energy field (vdw_energy_field) type: Field Type: Float: VdW Free Energy
    Default: VdW 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: integer: 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: 128
  • 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