Galaxy ABC MD Setup tutorial

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Workflow Type: Galaxy
Stable

AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es. Please, click here to access.

Based on the official GROMACS tutorial.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.

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).

Licensed under the Apache License 2.0, see the file LICENSE for details.

SEEK ID: https://workflowhub.eu/workflows/299?version=1

DOI: 10.48546/workflowhub.workflow.299.1

Inputs

ID Name Description Type
input_frcmod_path input_frcmod_path runtime parameter for tool LeapGenTop n/a
input_lib_path input_lib_path runtime parameter for tool LeapGenTop n/a
input_params_path input_params_path runtime parameter for tool LeapGenTop n/a
input_pdb_path input_pdb_path runtime parameter for tool LeapGenTop n/a
input_source_path input_source_path runtime parameter for tool LeapGenTop n/a
input_frcmod_path input_frcmod_path runtime parameter for tool LeapSolvate n/a
input_lib_path input_lib_path runtime parameter for tool LeapSolvate n/a
input_params_path input_params_path runtime parameter for tool LeapSolvate n/a
input_source_path input_source_path runtime parameter for tool LeapSolvate n/a
input_frcmod_path input_frcmod_path runtime parameter for tool LeapAddIons n/a
input_lib_path input_lib_path runtime parameter for tool LeapAddIons n/a
input_params_path input_params_path runtime parameter for tool LeapAddIons n/a
input_source_path input_source_path runtime parameter for tool LeapAddIons n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a
input_cpin_path input_cpin_path runtime parameter for tool SanderMdrun n/a
input_mdin_path input_mdin_path runtime parameter for tool SanderMdrun n/a

Steps

ID Name Description
0 LeapGenTop biobb_amber_leap_gen_top_ext
1 LeapSolvate biobb_amber_leap_solvate_ext
2 LeapAddIons biobb_amber_leap_add_ions_ext
3 ParmedHmassrepartition biobb_amber_parmed_hmassrepartition_ext
4 CpptrajRandomizeIons biobb_amber_cpptraj_randomize_ions_ext
5 SanderMdrun Step1 biobb_amber_sander_mdrun_ext
6 SanderMdrun Step2 NVT biobb_amber_sander_mdrun_ext
7 ProcessMinout biobb_amber_process_minout_ext
8 SanderMdrun Step3 biobb_amber_sander_mdrun_ext
9 ProcessMdout biobb_amber_process_mdout_ext
10 SanderMdrun Step4 biobb_amber_sander_mdrun_ext
11 ProcessMinout biobb_amber_process_minout_ext
12 SanderMdrun Step5 biobb_amber_sander_mdrun_ext
13 ProcessMinout biobb_amber_process_minout_ext
14 SanderMdrun Step6 NPT biobb_amber_sander_mdrun_ext
15 ProcessMinout biobb_amber_process_minout_ext
16 SanderMdrun Step7 NPT biobb_amber_sander_mdrun_ext
17 ProcessMdout biobb_amber_process_mdout_ext
18 SanderMdrun Step8 NPT biobb_amber_sander_mdrun_ext
19 ProcessMdout biobb_amber_process_mdout_ext
20 ProcessMdout biobb_amber_process_mdout_ext
21 SanderMdrun Step9 NPT biobb_amber_sander_mdrun_ext
22 ProcessMdout biobb_amber_process_mdout_ext
23 SanderMdrun Step10 NPT biobb_amber_sander_mdrun_ext
24 ProcessMdout biobb_amber_process_mdout_ext
25 SanderMdrun Free biobb_amber_sander_mdrun_ext

Outputs

ID Name Description Type
output_pdb_path output_pdb_path n/a
output_top_path output_top_path n/a
output_crd_path output_crd_path n/a
output_pdb_path output_pdb_path n/a
output_top_path output_top_path n/a
output_crd_path output_crd_path n/a
output_pdb_path output_pdb_path n/a
output_top_path output_top_path n/a
output_crd_path output_crd_path n/a
output_top_path output_top_path n/a
output_pdb_path output_pdb_path n/a
output_crd_path output_crd_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a
output_dat_path output_dat_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a
output_dat_path output_dat_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a
output_dat_path output_dat_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a
output_dat_path output_dat_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a
output_dat_path output_dat_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a
output_dat_path output_dat_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a
output_dat_path output_dat_path n/a
output_dat_path output_dat_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a
output_dat_path output_dat_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a
output_dat_path output_dat_path n/a
output_log_path output_log_path n/a
output_traj_path output_traj_path n/a
output_rst_path output_rst_path n/a
output_cpout_path output_cpout_path n/a
output_cprst_path output_cprst_path n/a
output_mdinfo_path output_mdinfo_path n/a

Version History

Version 2 (latest) Created 23rd Nov 2022 at 09:03 by Genís Bayarri

No revision comments

Frozen Version-2 5650af6

Version 1 (earliest) Created 29th Mar 2022 at 11:43 by Genís Bayarri

Initial commit


Frozen Version-1 8592492
help Creators and Submitter
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BioExcel Workflows
Galaxy
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Citation
Hospital, A., & Bayarri, G. (2022). Galaxy ABC MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.299.1
License
Apache Software License 2.0
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Views: 495

Created: 29th Mar 2022 at 11:43

Last used: 4th Dec 2022 at 21:53

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