Perform Weighted Ensemble MD Analysis

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/Molecular Dynamics

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation/Enhanced Sampling

  • Solution-based/Target Identification/Target Preparation/Pocket Detection

  • Solution-based/Hit to Lead/Target Preparation/Cryptic Pocket Detection

  • Role-based/Computational Chemist

  • Task-based/Target Prep & Analysis/Pocket Detection

Description

This floe performs analysis to evaluate structural integrity of conformations sampled by Weighted Ensemble simulations. The analysis includes calculation of fraction of native contacts and RMSD of conformational snapshots with respect to the initial conformation. Fraction of native contacts or RMSD values are then mapped onto the progress coordinates grid. In previous versions, this floe was named A4. Check for Protein Denaturation.

Promoted Parameters

Title in user interface (promoted name)

Input Data

Protein Sampling Data (collection): This is a ‘’Protein Sampling Data’’ output generated by ‘Run a Weighted Ensemble MD Simulation’ or ‘Continue a Weighted Ensemble MD Simulation’. The collection should come from the most recent Protein Sampling job run for a given protein.

  • Required

  • Type: collection_source

Output Data

Floe Report Output Collection (floe_report_out_a4):

  • Required

  • Type: string

  • Default: Weighted Ensemble MD Analysis Floe Report

Parameters for Free Energy Maps/Surfaces (optional)

Selection String (selstr_a4): Selection strings for defining a subset of the structure to be used to perform the trajectory analysis (NC fraction and RMSD analysis). The general syntax follows “[chain_id:][from_res_num][~to_res_num]”. Multiple residue ranges are supported by inputting multiple entries.

  • Type: string

Atoms selection modifier (select_modifier_a4): Additional selection criteria added to all chain segments chosen in chain selector

  • Type: string

  • Default: protein

  • Choices: [‘protein’, ‘backbone’, ‘name == CA’, ‘sidechain’]

Apply Weight (weight_option): Apply weights from WE-MD simulations when generating free energy maps.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Number of Histogram Bins (number_bins): Number of bins for plotting density distribution.

  • Type: integer

  • Default: 100

Maximum Free Energy Value (max_free_energy): Maximum value (in kcal/mol) for showing the 2D free energy map.

  • Type: decimal

  • Default: 50.0

Native Contact Map (is_ncfractions_on): Defines whether to plot the projection of the fraction of native contacts compared to the reference structure. The projection shows the average fraction of native contacts for all selected conformations for a given progress coordinate (pair).

  • Type: boolean

  • Default: True

  • Choices: [True, False]

RMSD Map (is_rmsd_on): Defines whether to plot the projection of the backbone root mean square deviation (RMSD) compared to the reference structure. The projection shows the average RMSD for all selected conformations for a given progress coordinate (pair).

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Selection Range for Trajectories

Start Iteration (a4_start_iteration): Iteration number for starting analysis of Weighted Ensemble MD simulation trajectories.

  • Type: integer

  • Default: 1

End Iteration (a4_end_iteration): Iteration number for ending analysis of Weighted Ensemble MD simulation trajectories.

  • Type: integer

Stride (a4_stride): Integer factor by which to subsample frames. (Only every stride-th frame will be read.)

  • Type: integer

  • Default: 1

A4 RMSF Analysis Memory (MB) (a4_rmsf_memory): The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.

  • Type: decimal

  • Default: 1800