Jupyter Notebook Protein Ligand Complex MD Setup tutorial

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Summary

This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels, nglview, ipywidgets, os, plotly, and simpletraj. Environment can be setup using the included environment.yml file.

Parameters

Inputs

Parameters needed to configure the workflow:

  • pdbCode: PDB code of the protein-ligand complex structure (e.g. 3HTB)

  • ligandCode: Small molecule 3-letter code for the ligand structure (e.g. JZ4)

  • mol_charge: Charge of the small molecule, needed to add hydrogen atoms.

Outputs

Output files generated (named according to the input parameters given above):

  • output_md_gro: final structure of the MD setup protocol

  • output_md_trr: final trajectory of the MD setup protocol

  • output_md_cpt: final checkpoint file

  • output_gppmd_tpr: final tpr file

  • output_genion_top_zip: final topology of the MD system

SEEK ID: https://workflowhub.eu/workflows/56?version=2

DOI: 10.48546/workflowhub.workflow.56.2

Version History

Version 7 (latest) Created 4th Mar 2024 at 14:23 by Genís Bayarri

Update to BioBB 4.1.*


Frozen Version-7 70dfb75

Version 6 Created 26th Jul 2023 at 10:21 by Genís Bayarri

Fixed importlib_metadata bug


Frozen Version-6 3b0b8b7

Version 5 Created 14th Apr 2023 at 09:04 by Genís Bayarri

Update to BioBB 4.0.*


Frozen Version-5 1a1f58d

Version 4 Created 15th Sep 2022 at 12:04 by Genís Bayarri

Update to BioBB 3.8.*. taken from Git commit 29a9ec9


Frozen Version-4 99d4200

Version 3 Created 2nd Jul 2021 at 09:43 by Douglas Lowe

Updated to BioBB 3.6.0. Taken from Git commit 513b6af


Frozen Version-3 9f15c63

Version 2 Created 6th May 2021 at 16:40 by Douglas Lowe

Updated for GROMACS 2020.4 and BioExcel Building Blocks version 3.5. Taken from Git commit 7e89a16


Frozen master 14efaa7

Version 1 (earliest) Created 22nd Sep 2020 at 16:30 by Douglas Lowe

Initial Upload. Taken from Git commit b4eee4f


Frozen master 877b1b7
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Citation
Lowe, D., & Bayarri, G. (2021). Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb) (jupyter notebook). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.56.2
License
Apache Software License 2.0
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Views: 5983

Created: 22nd Sep 2020 at 16:30

Last updated: 14th Apr 2023 at 09:05

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