Nonequilibrium Switching Recovery [Utility] [FECalc]

Description

  • Purpose:

    • This Floe allows for the recovery of nonequilibrium switching (NES) results in case the NES Floe hangs.

  • Method Recommendations/Requirements:

    • Two primary inputs are required; one additional primary input is optional. All other fields are supplementary: * The recovery file from the NES Floe that hung. * Orion dataset(s) containing equilibrium run data for each bound ligand participating in the NES run. * [Optional] Select experimental binding affinities from the Orion dataset containing equilibrium run data in the bound state, or supply a text file containing ligand names, affinity values, optional uncertainties, and optional units.

  • Expertise Level:

    • Regular

  • Compute Resource:

    • Minimal

  • Keywords:

    • Utility, FECalc

  • Related Floes:

    • Nonequilibrium Switching [MD] [FECalc]

    • Equilibrium and Nonequilibrium Switching [MDPrep] [MD] [FECalc]

This Floe is used to recover the NES results in case the NES Floe hangs. Using as input the recovery file from NES, it will finish off the analysis of the NES results to produce the same output datasets and NES. The analysis will be based only on the data in the recovery file.

Promoted Parameters

Title in user interface (promoted name)

Inputs

NES Recovery File (recovery): NES Recovery Input File

  • Required

  • Type: file_in

Bound Input Dataset (bound): with default naming, this input will be named MD_Bnd_Anlys or MD_Bnd in an upstream Floe

  • Required

  • Type: data_source

Experimental Affinities (From Bound Input Dataset)

Column in the dataset with experimental affinity values (affinity_column): Populated after selecting the dataset.

  • Type: field_parameter::float

  • Default: —

Units for affinity values (units):

Use ‘log’ for pIC50, pKi, etc.

  • Type: string

  • Default: Not selected

  • Choices: [‘Not selected’, ‘kcal/mol’, ‘kJ/mol’, ‘pM’, ‘nM’, ‘uM’, ‘mM’, ‘M’, ‘log’]

Column in the dataset with experimental affinity uncertainties (affinity_error_column): Populated after selecting the dataset.

  • Type: field_parameter::float

  • Default: —

Experimental Affinities (From Text File)

Text file containing experimental affinities (exp):

Syntax for ASCII file: [Ligand] [Affinity] [Error {optional}] [units {optional}]. Allowed units: kcal/mol, kJ/mol, log, M, mM, uM, nM, pM. Use ‘log’ for pIC50, pKi, etc. Use ‘M’, ‘mM’, ‘uM’, ‘nM’ or ‘pM’ for IC50, Ki, etc.

  • Type: file_in

Delimiter (field_separator): Whitespace (including tabs) or comma. Delimiters cannot be mixed.

  • Type: string

  • Default: whitespace(s)

  • Choices: [‘whitespace(s)’, ‘,’]

Units for affinity values (units_expt_file):

Use ‘log’ for pIC50, pKi, etc. Units present in the experimental file override this selection.

  • Type: string

  • Default: Not selected

  • Choices: [‘Not selected’, ‘kcal/mol’, ‘kJ/mol’, ‘pM’, ‘nM’, ‘uM’, ‘mM’, ‘M’, ‘log’]

Outputs

NES Output Dataset (out): Output dataset of NES.

  • Required

  • Type: dataset_out

  • Default: nes_output_dataset

Affinity Output Dataset (DG): Output dataset of binding affinity calculations.

  • Required

  • Type: dataset_out

  • Default: binding_affinity_output_dataset

NES Failure Dataset (fail): Output dataset of failed calculations.

  • Required

  • Type: dataset_out

  • Default: failed_dataset