Galaxy Amber Protein MD Setup tutorial

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

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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/297?version=1

DOI: 10.48546/workflowhub.workflow.297.1

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_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 Type
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

Version History

Version 2 (latest) Created 23rd Nov 2022 at 13:28 by Genís Bayarri

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Frozen Version-2 4f14959

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

Initial commit


Frozen Version-1 77500af
help Creators and Submitter
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Discussion Channels
BioExcel Workflows
Tutorial
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Citation
Hospital, A., & Bayarri, G. (2022). Galaxy Amber Protein MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.297.1
License
Apache Software License 2.0
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Views: 472

Created: 25th Mar 2022 at 10:10

Last used: 5th Dec 2022 at 07:35

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