Summary
This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).
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, 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. 1AKI)
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
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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 6 (latest) Created 4th Mar 2024 at 14:12 by Genís Bayarri
Update to BioBB 4.1.*
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Version-6
bab3b25
Version 5 Created 26th Jul 2023 at 10:17 by Genís Bayarri
Fixed importlib_metadata bug
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Version-5
f86759d
Version 4 Created 13th Apr 2023 at 16:35 by Genís Bayarri
Update to BioBB 4.0.*
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Version-4
efc1897
Version 3 Created 15th Sep 2022 at 10:24 by Genís Bayarri
Update to BioBB 3.8.*. taken from Git commit 77a78a
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Version-3
471a68f
Version 2 Created 1st Jul 2021 at 15:51 by Douglas Lowe
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Version-2
d4040dc
Version 1 (earliest) Created 7th May 2021 at 14:51 by Douglas Lowe
Uses GROMACS 2020.4 and BioExcel Building Blocks version 3.5. Taken from Git commit a81b483
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master
46c5b2e
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Views: 6183 Downloads: 1189
Created: 7th May 2021 at 14:51
Last updated: 13th Apr 2023 at 16:40
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