Complex Preparation

This cube assembles the complex made of a protein and its docked ligands. Each ligand must have just one conformer. In order to deal with multiple conformers, the ligands must be processed by the “ID Setting Cube” which will split ligand conformers in single conformer. In addition, each ligand needs to have a ligand ID that can be set by using the “ID Setting Cube” as well. The ligands must be docked to the target protein otherwise a runtime error will be raised. If crystallographic water molecules are present in the target protein, the water molecules that clashes with the docked ligands will be removed. The ligand is identified by the ligand residue name that can be set by using the cube parameter.

Calculation Parameters

  • lig_res_name (string) : The ligand residue name
    Default: LIG

Metrics

Cube Metric Parameters

  • Metric Period (decimal) : How often to sample metrics, in seconds
    Default: 60 Min: 1 Max: 300
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network

Hardware Parameters

Machine hardware requirements

  • Memory (MB) (decimal) : The minimum amount of memory this cube requires in MBs
    Default: 1800 Min: 256.0 Max: 8589934592
  • Temporary Disk Space (MB) (decimal) : The amount of disk space this cube requires in MBs
    Default: 5120.0 Min: 128.0 Max: 8589934592
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Instance Type (string) : The type of instance that this cube needs to be run on
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (string) : Only run on machines with matching tags (comma separated)
    Default: “”

Tip

filename: MDOrion/ComplexPrep/cubes.py