Extract Short Trajectory MD Results for Download [Utility]ΒΆ

Category Paths

  • Product-based/Molecular Dynamics

  • Role-based/Computational Chemist

  • Role-based/Medicinal Chemist

  • Task-based/Molecular Dynamics

  • Task-based/Affinity Prediction

  • Solution-based/Hit to Lead/Affinity Prediction/STMD

  • Solution-based/Small Molecule Lead-opt/Affinity

Description

  • Purpose:

    • This Floe extracts useful results generated from the analysis Floes for protein-ligand MD.

  • Method Recommendations/Requirements:

    • Required input is a Dataset output by the Analysis Floes:

      • Analyze Protein-Ligand MD

      • Short Trajectory MD with Analysis

  • Expertise Level:

    • Regular

  • Compute Resource:

    • Minimal

  • Keywords:

    • Utility

  • Related Floes:

    • Analyze Protein-Ligand MD

    • Short Trajectory MD with Analysis

This Floe extracts useful results generated from the Short Trajectory MD with Analysis Floe. The protein, ligand and binding site water trajectories are extracted with the protein and ligand average and median clusters. Also the generated HTML Floe report is saved. The MD Data is uploaded as a .tar.gz file to S3 and it is available under the Files UI tab in Orion with the user-selected file name.

Promoted Parameters

Title in user interface (promoted name)

  • Failed Dataset (fail) type: dataset_out: Output dataset of failed calculations
    Default: failed_dataset
  • MD Analysis Input Dataset (in) type: data_source: The Dataset produced by MD Analysis floe
  • Output Tarball File (out_file_name) type: string: Output Tarball File name
    Default: md_data.tar.gz