Activesite Ligand Restrained Minimization

This cube performs a restrained minimization of the input ligand,

in the presence of a protein. A harmonic constraint is placed around the ligand heavy atoms to restrict movement of the atoms. This is useful as an initial step when optimizing a ligand while preserving it’s pose.

The minimized molecule conformers are added to the intake port record and emitted through the success port.

Related Cubes

Calculation Parameters

  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Temporary Disk Space (MiB) (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
  • Force field (string) : Force field model to be used. Built-in types are: MMFF94S, Smirnoff99Frost, PARSLEY_OPENFF100, PARSLEY_OPENFF111, PARSLEY_OPENFF120. The name of a .offxml file that defines a SMIRNOFF force field can also be used as input.
    Default: MMFF94S
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • None (decimal) : Harmonic constraint potential constant
    Default: 1.0 Min: 0.0001 Max: 100.0
  • None (decimal) : Harmonic constraint distance constant
    Default: 0.0 Max: 1.0
  • Instance Tags (string) : Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (string) : The type of instance that this cube needs to be run on
  • Max Rotors (integer) : Cutoff of rotatable bonds. The cube will skip molecules with rotors more than the cutoff.
    Default: 20 Min: 1 Max: 9999
  • Memory (MiB) (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 (decimal) : How often to sample metrics, in seconds
    Default: 60 Min: 1 Max: 300
  • Solvent model (string) : Solvent model to be used
    Default: Gas-phase
    Choices: Gas-phase, PB
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required

Field parameters

  • Energy field (Field Type: Float) : Total energy of the molecule conformer
    Default: Energy
  • None (Field Type: StringVec) : Message extended log field
    Default: Extended Log Field
  • None (Field Type: Chem.Mol) :
  • Protein Field (Field Type: Chem.Mol) :
  • None (Field Type: String) : Message log field
    Default: Log Field
  • None (Field Type: Chem.Mol) :

Hardware Parameters

Machine hardware requirements

  • Memory (MiB) (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
  • Temporary Disk Space (MiB) (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 (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: “”

Metrics Parameters

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

Parallel Activesite Ligand Restrained Minimization

The parallel version adds these extra parameters.

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

Tip

filename: snowball/szybki/activesite_ligand_min.py