Python Amber Automatic Ligand Parameterization tutorial using BioExcel Building Blocks (biobb)
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1yr ago
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Version 2
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Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)
This tutorial aims 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.
Code Snippets
5 | from biobb_common.configuration import settings |
7 8 | from biobb_chemistry.babelm.babel_minimize import babel_minimize from biobb_chemistry.acpype.acpype_params_ac import acpype_params_ac |
18 | babel_minimize(**global_paths["step2_babel_minimize"], properties=global_prop["step2_babel_minimize"]) |
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Created: 1yr ago
Updated: 1yr ago
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https://workflowhub.eu/workflows/292
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python-amber-automatic-ligand-parameterization-tut
Version:
Version 2
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