CWL GMX Automatic Ligand Parameterization tutorial Version 1
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Download RO CrateAutomatic 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.
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).
- (c) 2015-2022 Barcelona Supercomputing Center
- (c) 2015-2022 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| step2_babel_minimize_config | n/a | n/a |
|
| step2_babel_minimize_input_path | n/a | n/a |
|
| step2_babel_minimize_output_path | n/a | n/a |
|
| step3_acpype_params_gmx_config | n/a | n/a |
|
| step3_acpype_params_gmx_output_path_gro | n/a | n/a |
|
| step3_acpype_params_gmx_output_path_itp | n/a | n/a |
|
| step3_acpype_params_gmx_output_path_top | n/a | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| step2_babel_minimize | BabelMinimize | Energetically minimize small molecules. |
| step3_acpype_params_gmx | AcpypeParamsGMX | Small molecule parameterization for GROMACS MD package. |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| step2_babel_minimize_out1 | output_path | Path to the output file |
|
| step3_acpype_params_gmx_out1 | output_path_gro | Path to the GRO output file |
|
| step3_acpype_params_gmx_out2 | output_path_itp | Path to the ITP output file |
|
| step3_acpype_params_gmx_out3 | output_path_top | Path to the TOP output file |
|
Version History
Version 1 (earliest) Created 10th Jan 2022 at 10:39 by Genís Bayarri
Fetched ligand.pdb from URL
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Creators and Submitter
Views: 905 Downloads: 2
Created: 10th Jan 2022 at 10:39
Last updated: 17th Mar 2022 at 14:06
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https://orcid.org/0000-0003-0513-0288
BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...
Space: BioExcel
Public web page: https://mmb.irbbarcelona.org/biobb/
