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:
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pdbCode: PDB code of the protein-ligand complex structure (e.g. 3HTB)
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ligandCode: Small molecule 3-letter code for the ligand structure (e.g. JZ4)
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mol_charge: Charge of the small molecule, needed to add hydrogen atoms.
Outputs
Output files generated (named according to the input parameters given above):
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output_md_gro: final structure of the MD setup protocol
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output_md_trr: final trajectory of the MD setup protocol
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output_md_cpt: final checkpoint file
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output_gppmd_tpr: final tpr file
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output_genion_top_zip: final topology of the MD system
Version History
Version 7 (latest) Created 4th Mar 2024 at 14:23 by Genís Bayarri
Update to BioBB 4.1.*
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Version-7
70dfb75
Version 6 Created 26th Jul 2023 at 10:21 by Genís Bayarri
Fixed importlib_metadata bug
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Version-6
3b0b8b7
Version 5 Created 14th Apr 2023 at 09:04 by Genís Bayarri
Update to BioBB 4.0.*
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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
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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
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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
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master
14efaa7
Version 1 (earliest) Created 22nd Sep 2020 at 16:30 by Douglas Lowe
Initial Upload. Taken from Git commit b4eee4f
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master
877b1b7
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Views: 8757 Downloads: 1784
Created: 22nd Sep 2020 at 16:30
Last updated: 14th Apr 2023 at 09:05
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