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.

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_source_path	input_source_path	runtime parameter for tool LeapGenTop	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_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_ref_path	input_ref_path	runtime parameter for tool SanderMdrun	n/a
input_exp_path	input_exp_path	runtime parameter for tool CpptrajRms	n/a

Steps

ID	Name	Description
0	Pdb	biobb_io_pdb_ext
1	Pdb4amberRun	biobb_amber_pdb4amber_run_ext
2	LeapGenTop	biobb_amber_leap_gen_top_ext
3	SanderMdrun MinH	biobb_amber_sander_mdrun_ext
4	AmberToPdb	biobb_amber_amber_to_pdb_ext
5	SanderMdrun MinSys	biobb_amber_sander_mdrun_ext
6	ProcessMinout	biobb_amber_process_minout_ext
7	LeapSolvate	biobb_amber_leap_solvate_ext
8	ProcessMinout	biobb_amber_process_minout_ext
9	LeapAddIons	biobb_amber_leap_add_ions_ext
10	SanderMdrun Energy Min	biobb_amber_sander_mdrun_ext
11	SanderMdrun Warm Up	biobb_amber_sander_mdrun_ext
12	ProcessMinout	biobb_amber_process_minout_ext
13	SanderMdrun NVT	biobb_amber_sander_mdrun_ext
14	ProcessMdout	biobb_amber_process_mdout_ext
15	SanderMdrun NPT	biobb_amber_sander_mdrun_ext
16	ProcessMdout	biobb_amber_process_mdout_ext
17	SanderMdrun Free	biobb_amber_sander_mdrun_ext
18	ProcessMdout	biobb_amber_process_mdout_ext
19	CpptrajRms First	biobb_analysis_cpptraj_rms_ext
20	CpptrajRms Exp	biobb_analysis_cpptraj_rms_ext
21	CpptrajRgyr	biobb_analysis_cpptraj_rgyr_ext
22	CpptrajImage	biobb_analysis_cpptraj_image_ext

Outputs

ID	Name	Description
output_pdb_path	output_pdb_path	n/a
output_pdb_path	output_pdb_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_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_pdb_path	output_pdb_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_pdb_path	output_pdb_path	n/a
output_top_path	output_top_path	n/a
output_crd_path	output_crd_path	n/a
output_dat_path	output_dat_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_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_cpptraj_path	output_cpptraj_path	n/a
output_cpptraj_path	output_cpptraj_path	n/a
output_cpptraj_path	output_cpptraj_path	n/a
output_cpptraj_path	output_cpptraj_path	n/a

Galaxy Amber Protein MD Setup tutorial
Version 1

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

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

Copyright & Licensing

Inputs

Steps

Outputs

Version History

Version 1 (earliest) Created 25th Mar 2022 at 10:10 by Genís Bayarri

Creators

Submitter

Galaxy Amber Protein MD Setup tutorial Version 1

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

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

Copyright & Licensing

Inputs

Steps

Outputs

Version History

Version 1 (earliest) Created 25th Mar 2022 at 10:10 by Genís Bayarri

Creators

Submitter

Related items

Galaxy Amber Protein MD Setup tutorial
Version 1