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 modifier to specify required group of atoms for PMF, RMSD and NC-fractions
Type: string
Default: protein
Choices: [‘protein’, ‘backbone’, ‘alpha-carbons’, ‘sidechain’]
Apply Weight (is_weight_on): Apply weights from WEMD 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 Potential of Mean Force Value (max_free_energy): Maximum on color scale (in kcal/mol) for 2D colormap of pPotential of mean force.
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 (first_iter): The start iteration of WE segments to be extracted. Leave empty to extract from the first iteration that is available.
Type: integer
End Iteration (last_iter): The end iteration of WE segments to be extracted. Leave empty to stop extracting at the last iteration that is available.
Type: integer
Endpoint Only (endpoint_only): Use either final trajectory configuration on each WEMD segment or all of them.
Required
Type: boolean
Default: True
Choices: [True, False]
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: 8192