Summary
Jupyter Notebook containing a tutorial to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.
OpenBabel and ACPype packages are used to add hydrogens, energetically minimize the structure, and generate parameters for the GROMACS package. With Generalized Amber Force Field (GAFF) forcefield and AM1-BCC charges.
Parameters
Inputs:
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ligandCode: 3-letter code of the ligand structure (e.g. IBP)
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mol_charge: Molecule net charge (e.g. -1)
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pH: Acidity or alkalinity for the small molecule. Hydrogen atoms will be added according to this pH. (e.g. 7.4)
Outputs
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IBPparams.gro: Structure of the parameterized ligand in gro (GROMACS) format.
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IBPparams.top: Topology of the parameterized ligand, including a reference to the IBPparams.itp.
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IBPparams.itp: Include Topology File (itp) of the parameterized ligand, including the parameters information: bonds, angles, dihedrals, etc.
Additional Resources
Version History
Version 6 (latest) Created 4th Mar 2024 at 14:20 by Genís Bayarri
Update to BioBB 4.1.*
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Version-6
f2526d7
Version 5 Created 26th Jul 2023 at 10:20 by Genís Bayarri
Fixed importlib_metadata bug
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Version-5
62173bf
Version 4 Created 14th Apr 2023 at 08:51 by Genís Bayarri
Update to BioBB 4.0.*
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Version-4
a3814ff
Version 3 Created 15th Sep 2022 at 11:59 by Genís Bayarri
Update to BioBB 3.8.*. taken from Git commit 2a351bf
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Version-3
0e1ae08
Version 2 Created 29th Jun 2021 at 08:40 by Robin Long
Updated to BioBB 3.6.0. Taken from Git commit 461262dae
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Version-2
461262d
Version 1 (earliest) Created 14th Sep 2020 at 11:01 by Robin Long
Initial Commit. Taken from Git commit c6cb736
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master
eff4a17
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Created: 14th Sep 2020 at 11:01
Last updated: 5th Mar 2024 at 09:40
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