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BioExcel AMBER Constant pH MD Setup - BPTI 6PTI
W-16 · AMBER Constant pH MD Setup
v116 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.
- 01Download 6PTI structure from PDB
- Consumes
- fetch_pdb_config, src_conda_env_yaml
- Produces
- downloaded_pdb
- 02Prepare PDB for constant pH AMBER (pdb4amber)
- Consumes
- pdb4amber_config, downloaded_pdb
- Produces
- pdb4amber_pdb
- 03Create protein system topology with ff14SB and constph (leap)
- Consumes
- leap_gen_top_config, pdb4amber_pdb
- Produces
- top_pdb, top_top, top_crd
- 04Create truncated octahedron solvent box (leap)
- Consumes
- leap_solvate_config, top_pdb
- Produces
- solv_pdb, solv_top, solv_crd
- 05Neutralize and add ions (leap)
- Consumes
- leap_add_ions_config, solv_pdb
- Produces
- ions_pdb, ions_top, ions_crd
- 06Generate constant pH input file (cpinutil)
- Consumes
- parmed_cpinutil_config, ions_top
- Produces
- cpin_path, cph_top
- 07Energy minimize the system with backbone restraints (sander)
- Consumes
- sander_min_config, cph_top, ions_crd
- Produces
- min_traj, min_rst, min_log
- 08Extract minimization energy (process_minout)
- Consumes
- process_min_config, min_log
- Produces
- min_dat
- 09Heat the system from 0 to 300 K (sander)
- Consumes
- sander_heat_config, cph_top, min_rst
- Produces
- heat_traj, heat_rst, heat_log
- 10Extract heating temperature (process_mdout)
- Consumes
- process_heat_config, heat_log
- Produces
- heat_dat
- 11Equilibrate the system NVT (sander)
- Consumes
- sander_nvt_config, cph_top, heat_rst
- Produces
- nvt_traj, nvt_rst, nvt_log
- 12Extract NVT equilibration temperature (process_mdout)
- Consumes
- process_nvt_config, nvt_log
- Produces
- nvt_dat
- 13Equilibrate the system NPT (sander)
- Consumes
- sander_npt_config, cph_top, nvt_rst
- Produces
- npt_traj, npt_rst, npt_log
- 14Extract NPT pressure and density (process_mdout)
- Consumes
- process_npt_config, npt_log
- Produces
- npt_dat
- 15Constant pH MD simulation (sander)
- Consumes
- sander_cph_free_config, cph_top, npt_rst, cpin_path
- Produces
- ph_traj, ph_rst, ph_cpout, ph_cprst, ph_log, ph_mdinfo
- 16Analyse protonation states and predict pKa values (cphstats)
- Consumes
- cphstats_config, cpin_path, ph_cpout
- Produces
- ph_dat, ph_pop
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.