Galaxy ABC MD Setup tutorial
Version 1

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Workflow Type: Galaxy

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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

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
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