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.

Inputs

ID Name Description Type
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_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_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 RemovePdbWater biobb_structure_utils_remove_pdb_water_ext
2 RemoveLigand PO4 biobb_structure_utils_remove_ligand_ext
3 RemoveLigand BME biobb_structure_utils_remove_ligand_ext
4 Pdb4amberRun biobb_amber_pdb4amber_run_ext
5 ExtractHeteroatoms biobb_structure_utils_extract_heteroatoms_ext
6 ReduceAddHydrogens biobb_chemistry_reduce_add_hydrogens_ext
7 BabelMinimize biobb_chemistry_babel_minimize_ext
8 AcpypeParamsAc biobb_chemistry_acpype_params_ac_ext
9 LeapGenTop biobb_amber_leap_gen_top_ext
10 SanderMdrun MinH biobb_amber_sander_mdrun_ext
11 ProcessMinout biobb_amber_process_minout_ext
12 SanderMdrun MinSys biobb_amber_sander_mdrun_ext
13 AmberToPdb biobb_amber_amber_to_pdb_ext
14 ProcessMinout biobb_amber_process_minout_ext
15 LeapSolvate biobb_amber_leap_solvate_ext
16 LeapAddIons biobb_amber_leap_add_ions_ext
17 SanderMdrun Energy Min biobb_amber_sander_mdrun_ext
18 ProcessMinout biobb_amber_process_minout_ext
19 SanderMdrun Warm Up biobb_amber_sander_mdrun_ext
20 ProcessMdout biobb_amber_process_mdout_ext
21 SanderMdrun NVT biobb_amber_sander_mdrun_ext
22 ProcessMdout biobb_amber_process_mdout_ext
23 SanderMdrun NPT biobb_amber_sander_mdrun_ext
24 ProcessMdout biobb_amber_process_mdout_ext
25 SanderMdrun Free biobb_amber_sander_mdrun_ext
26 CpptrajRms First biobb_analysis_cpptraj_rms_ext
27 CpptrajRms Exp biobb_analysis_cpptraj_rms_ext
28 CpptrajRgyr biobb_analysis_cpptraj_rgyr_ext
29 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_structure_path output_structure_path n/a
output_structure_path output_structure_path n/a
output_pdb_path output_pdb_path n/a
output_heteroatom_path output_heteroatom_path n/a
output_path output_path n/a
output_path output_path n/a
output_path_frcmod output_path_frcmod n/a
output_path_inpcrd output_path_inpcrd n/a
output_path_lib output_path_lib n/a
output_path_prmtop output_path_prmtop 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_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_pdb_path output_pdb_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_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_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_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 08:43 by Genís Bayarri

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Frozen Version-2 a4afa1e

Version 1 (earliest) Created 25th Mar 2022 at 11:42 by Genís Bayarri

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Frozen Version-1 000da69
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Created: 25th Mar 2022 at 11:42

Last used: 8th Dec 2022 at 17:05

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