Galaxy Amber Protein MD Setup tutorial
Version 1

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.

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

Initial commit


Open master 77500af
help Creators and Submitter
Activity

Views: 178

Created: 25th Mar 2022 at 10:10

Last used: 28th Jun 2022 at 19:33

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