Summary
This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial.
Workflow engine is a jupyter notebook. Auxiliary libraries used are nb_conda_kernels, os, and plotly. Environment setup can be carried out using the environment.yml in the code repository. The tutorial uses docker for running pmx - a local setup can be used instead, see notes in the tutorial.
Parameters
Inputs
Workflow Input files needed:
-
stateA_traj: Equilibrium trajectory for the WT protein.
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stateB_traj: Equilibrium trajectory for the Mutated protein.
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stateA_tpr: WT protein topology (GROMACS tpr format).
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stateB_tpr: Mutated protein topology (GROMACS tpr format).
Auxiliar force field libraries needed:
- mutff45 (folder): pmx mutation force field libraries.
Outputs
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pmx.outputs: Final free energy estimation. Summary of information got applying the different methods.
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pmx.plots.png: Final free energy plot of the Mutation free energy pipeline.
Version History
Version 6 (latest) Created 4th Mar 2024 at 14:26 by Genís Bayarri
Update to BioBB 4.1.*
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Version-6
3706360
Version 5 Created 26th Jul 2023 at 10:23 by Genís Bayarri
Fixed importlib_metadata bug
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Version-5
098c09d
Version 4 Created 16th Sep 2022 at 10:35 by Genís Bayarri
Update to BioBB 3.8.*. taken from Git commit 5b20069
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Version-4
a9f9ac3
Version 3 Created 1st Jul 2021 at 11:33 by Douglas Lowe
Updated to BioBB 3.6.0. Taken from Git commit f329e83
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Version-3
8659eeb
Version 2 Created 7th May 2021 at 14:22 by Douglas Lowe
Updated for GROMACS 2020.4 and BioExcel Building Blocks version 3.5. Taken from Git commit ba3c37d
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master
f14839e
Version 1 (earliest) Created 15th Sep 2020 at 12:56 by Douglas Lowe
Initial commit. Taken from Git commit 3272c52
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master
d778945
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Created: 15th Sep 2020 at 12:56
Last updated: 5th Mar 2024 at 09:41
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