Calculate Normal Modes¶
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 identifies the normal modes associated with the input conformation and generates a dataset containing top 20 normal modes with high ‘Mode Collectivity’ and ‘Variance’. These modes are mapped on a design unit that can be viewed via the 3D or Analyze pages on Orion. One or two selected normal modes are intended as input to a ‘Protein Sampling’ floe, and we suggest choosing from modes with a high ‘Mode Collectivity’ value.
Promoted Parameters
Title in user interface (promoted name)
Input Data
Solvated and Equilibrated Protein (in): The ‘Solvated and Equilibrated Protein’ dataset output from the ‘Solvate and Equilibrate Target Protein’ floe.
Required
Type: data_source
Output Data
Output Dataset (a2_data_out): Dataset contaning protein normal modes, their mode collectivity and variance values.
Required
Type: dataset_out
Default: Protein Normal Modes
Failure Report (failure_report): Output report to generate upon failure.
Type: string
Default: Protein Normal Mode Failure Report
System Parameters
System Selection String (selstr): Selection strings for selecting a subset of the structure to be used to perform the ANM calculations (i.e., system). Use the design unit in the output dataset from the Solvate and Equilibrate Target Protein floe as a reference when selecting the residue and chains for the selection string(s). The general syntax follows “[chain_id]:[from_res_num]~[to_res_num]”. In practice this would look like “A:1~150” when selecting residues 1 to 150 on chain A of the input protein. Multiple residue ranges are supported by inputting multiple entries. See tutorial for more examples.
Type: string
Advanced System Parameters
System-Environment Framework (sys_env_method):
Method for performing the system-environment calculations. Slice: simply extract the specified portion (i.e., system) of the entire motion. The resulting modes are normalized but their orthogonality may be lost. The eigenvalue/variance of the modes are unaltered so they still correspond to the energy of the entirety, i.e., system and environment. Reduce: calculate system’s motion while taking account of the effects from the environment. The resulting modes are orthonormal and their eigenvalue/variance correspond to the energy of only the system part.
Type: string
Default: Reduce
Choices: [‘Disabled’, ‘Slice’, ‘Reduce’]
Environment Selection String (substr): Selection strings for selecting the environment for performing the system-environment analysis. Environment must include the system specified by “System Selection String”. Leave empty for selecting everything as the envrionment (default). Use the design unit in the output dataset from the Solvate and Equilibrate Target Protein floe as a reference when selecting the residue and chains for the selection string(s). The general syntax follows “[chain_id]:[from_res_num]~[to_res_num]”. In practice this would look like “A:1~150” when selecting residues 1 to 150 on chain A of the input protein. Multiple residue ranges are supported by inputting multiple entries.
Type: string
ANM Parameters
Spring Constant (gamma):
Spring Constant of the elastic network.
Type: decimal
Default: 1.0
Cutoff Distance (Å) (cutoff):
Cutoff distance for pairwise interactions.
Type: decimal
Default: 15.0
Mode Filtering Property (property): Which property mode filtering is based on.
Required
Type: string
Default: Collectivity
Choices: [‘Variance’, ‘Collectivity’]
Maximum Number of Selected Modes (num_selected_modes): Maximum number of modes to be selected. Leave empty for disabling filtering.
Type: integer