Freeform Ligand Strain

This cube calculates ligand strain associated with an input molecule’s conformers, with respect to the ensemble of free ligand solution conformers of the same molecule. This cube also reports the ensemble free energies.

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

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
  • Force Field (ff_type) type: string: Built-in force field model to be used.
    Default: sage
    Choices: mmff94s, parsley, sage
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Include input conformer (include_input) type: boolean: Flag to include the input conformers in ensemble. Setting this to true would add the input conformers to the internally generated conformers.
    Default: False
  • 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
  • Ionic state (ionic_state) type: string: Ionic state of molecules to be used
    Default: ph74
    Choices: ph74, uncharged, input
  • 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
  • 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
  • Output All Results (output_all_res) type: boolean: Output all available single conformer results. If set to False, only the more important results are reported
    Default: True
  • 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
  • Use input ensemble (use_inp_ens) type: boolean: Flag to use input ensemble conformers. Setting this to true would bypass any new conformer generation.
    Default: False

Field parameters

  • Delta G field (delta_g_field) type: Field Type: Float: Free energy of selecting the conformer from the ensemble
    Default: Delta G
  • Total entropy field (ens_ent_field) type: Field Type: Float: Total entropy of the conformer ensemble
    Default: Total entropy
  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • Global strain field (global_strain_field) type: Field Type: Float: Global strain associated with the conformer
    Default: GlobalStrain
  • None (in_mol_field) type: Field Type: Chem.Mol:
  • None (in_strain_mol_field) type: Field Type: Chem.Mol:
  • Intra-molecular energy field (intra_ene_field) type: Field Type: Float: Total intermolecular energy of the conformer
    Default: Intra-molecular energy
  • ln Qrot field (ln_qrot_field) type: Field Type: Float: Natural logarithm of the conformer rotational partition function
    Default: ln Qrot
  • ln Qvib field (ln_qvib_field) type: Field Type: Float: Natural logarithm of the conformer vibrational partition function
    Default: ln Qvib
  • Local strain field (local_strain_field) type: Field Type: Float: Local strain associated with the conformer
    Default: LocalStrain
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • None (out_ens_mol_field) type: Field Type: Chem.Mol: Output conformer ensemble
    Default: Ensemble
  • None (out_free_mol_field) type: Field Type: Chem.Mol: Output Free ligand for strain analysis
    Default: Free mol
  • None (out_mol_field) type: Field Type: Chem.Mol:
  • None (out_rstr_mol_field) type: Field Type: Chem.Mol: Output Restrained ligand for strain analysis
    Default: Restrained mol
  • Partner Conformer delta G (partner_dg_field) type: Field Type: Float: Delta G associated with the partner conformer
    Default: PartnerConfdG
  • Partner conformer relative energy (partner_erel_field) type: Field Type: Float: Relative energy associated with the partner conformer
    Default: PartnerConfErel
  • Partner conformer index field (partner_idx_field) type: Field Type: Int: Index of ensemble conformer associated with the conformer
    Default: PartnerConfIdx
  • Probability of state field (prob_field) type: Field Type: Float: Probability of state associated with the conformer
    Default: Probability of state
  • Relative energy field (rel_ene_field) type: Field Type: Float: Relative energy of the conformer with respect to the lowest energy conformer of the ensemble
    Default: Relative energy
  • Relative lnQ field (rel_lnq_field) type: Field Type: Float: Natural logarithm of the relative vibrational-rotational partition function with respect to the lowest free energy conformer in the ensemble
    Default: Relative lnQ
  • Rotational Entropy field (rot_ent_field) type: Field Type: Float: Rotational entropy of the conformer
    Default: Rotational Entropy
  • Solvation energy field (solv_ene_field) type: Field Type: Float: Solvation energy of the conformer
    Default: Solvation energy
  • Total energy field (tot_ene_field) type: Field Type: Float: Total (intramolecular + solvation) energy of the conformer
    Default: Total energy
  • Vibrational Entropy field (vib_ent_field) type: Field Type: Float: Vibrational entropy of the conformer
    Default: Vibrational Entropy

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

Parallel Freeform Ligand Strain

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