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Published workflow · Temple Compute
BioExcel Ligand Parameterization
W-04 · Ligand Parameterization
v14 stages0 clones0
The pipeline
Every stage picks its own compute target. Temple Compute OS resolves the dependencies between them and moves the data across each boundary.
- 01Fetch ligand structure from PDB
- Consumes
- fetch_ligand_config, src_conda_env_yaml
- Produces
- ligand_pdb
- 02Add hydrogen atoms (OpenBabel)
- Consumes
- add_h_config, ligand_pdb, src_conda_env_yaml
- Produces
- ligand_mol2
- 03Energetically minimize hydrogen atoms (OpenBabel GAFF)
- Consumes
- minimize_h_config, ligand_mol2, src_conda_env_yaml
- Produces
- minimized_pdb
- 04Generate GROMACS parameters (ACPype / GAFF)
- Consumes
- params_config, minimized_pdb, src_conda_env_yaml
- Produces
- params_gro, params_itp, params_top
Run this workflow
This release is frozen and self-contained: the pipeline definition, its input files, and its plugin environment. Open it in Temple Compute OS to clone it into your own account and run it on HPC or any cloud. Temple Compute OS is in private beta, so you will need an invitation first.