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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).
- (c) 2015-2023 Barcelona Supercomputing Center
- (c) 2015-2023 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
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 |
---|---|---|---|
mypdb.pdb | mypdb.pdb | n/a |
|
myremove_pdb_water.pdb | myremove_pdb_water.pdb | n/a |
|
myremove_ligand.pdb | myremove_ligand.pdb | n/a |
|
_anonymous_output_1 | _anonymous_output_1 | n/a |
|
mypdb4amber_run.pdb | mypdb4amber_run.pdb | n/a |
|
myextract_heteroatoms.pdb | myextract_heteroatoms.pdb | n/a |
|
myreduce_add_hydrogens.pdb | myreduce_add_hydrogens.pdb | n/a |
|
mybabel_minimize.mol2 | mybabel_minimize.mol2 | n/a |
|
myacpype_params_ac.prmtop | myacpype_params_ac.prmtop | n/a |
|
myacpype_params_ac.inpcrd | myacpype_params_ac.inpcrd | n/a |
|
myacpype_params_ac.frcmod | myacpype_params_ac.frcmod | n/a |
|
myacpype_params_ac.lib | myacpype_params_ac.lib | n/a |
|
myleap_gen_top.pdb | myleap_gen_top.pdb | n/a |
|
myleap_gen_top.top | myleap_gen_top.top | n/a |
|
myleap_gen_top.crd | myleap_gen_top.crd | n/a |
|
mysander_mdrun.log | mysander_mdrun.log | n/a |
|
mysander_mdrun.rst | mysander_mdrun.rst | n/a |
|
mysander_mdrun.cpout | mysander_mdrun.cpout | n/a |
|
mysander_mdrun.mdinfo | mysander_mdrun.mdinfo | n/a |
|
mysander_mdrun.cprst | mysander_mdrun.cprst | n/a |
|
mysander_mdrun.trj | mysander_mdrun.trj | n/a |
|
myprocess_minout.dat | myprocess_minout.dat | n/a |
|
_anonymous_output_2 | _anonymous_output_2 | n/a |
|
_anonymous_output_3 | _anonymous_output_3 | n/a |
|
_anonymous_output_4 | _anonymous_output_4 | n/a |
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_anonymous_output_5 | _anonymous_output_5 | n/a |
|
_anonymous_output_6 | _anonymous_output_6 | n/a |
|
_anonymous_output_7 | _anonymous_output_7 | n/a |
|
myamber_to_pdb.pdb | myamber_to_pdb.pdb | n/a |
|
_anonymous_output_8 | _anonymous_output_8 | n/a |
|
myleap_solvate.pdb | myleap_solvate.pdb | n/a |
|
myleap_solvate.parmtop | myleap_solvate.parmtop | n/a |
|
myleap_solvate.crd | myleap_solvate.crd | n/a |
|
myleap_add_ions.pdb | myleap_add_ions.pdb | n/a |
|
myleap_add_ions.crd | myleap_add_ions.crd | n/a |
|
myleap_add_ions.parmtop | myleap_add_ions.parmtop | n/a |
|
_anonymous_output_9 | _anonymous_output_9 | n/a |
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_anonymous_output_10 | _anonymous_output_10 | n/a |
|
_anonymous_output_11 | _anonymous_output_11 | n/a |
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_anonymous_output_12 | _anonymous_output_12 | n/a |
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_anonymous_output_13 | _anonymous_output_13 | n/a |
|
_anonymous_output_14 | _anonymous_output_14 | n/a |
|
_anonymous_output_15 | _anonymous_output_15 | n/a |
|
_anonymous_output_16 | _anonymous_output_16 | n/a |
|
_anonymous_output_17 | _anonymous_output_17 | n/a |
|
_anonymous_output_18 | _anonymous_output_18 | n/a |
|
_anonymous_output_19 | _anonymous_output_19 | n/a |
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_anonymous_output_20 | _anonymous_output_20 | n/a |
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_anonymous_output_21 | _anonymous_output_21 | n/a |
|
myprocess_mdout.dat | myprocess_mdout.dat | n/a |
|
_anonymous_output_22 | _anonymous_output_22 | n/a |
|
_anonymous_output_23 | _anonymous_output_23 | n/a |
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_anonymous_output_24 | _anonymous_output_24 | n/a |
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_anonymous_output_25 | _anonymous_output_25 | n/a |
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_anonymous_output_26 | _anonymous_output_26 | n/a |
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_anonymous_output_27 | _anonymous_output_27 | n/a |
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_anonymous_output_28 | _anonymous_output_28 | n/a |
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_anonymous_output_29 | _anonymous_output_29 | n/a |
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_anonymous_output_30 | _anonymous_output_30 | n/a |
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_anonymous_output_31 | _anonymous_output_31 | n/a |
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_anonymous_output_32 | _anonymous_output_32 | n/a |
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_anonymous_output_33 | _anonymous_output_33 | n/a |
|
_anonymous_output_34 | _anonymous_output_34 | n/a |
|
_anonymous_output_35 | _anonymous_output_35 | n/a |
|
_anonymous_output_36 | _anonymous_output_36 | n/a |
|
mysander_mdrun.netcdf | mysander_mdrun.netcdf | n/a |
|
_anonymous_output_37 | _anonymous_output_37 | n/a |
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_anonymous_output_38 | _anonymous_output_38 | n/a |
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_anonymous_output_39 | _anonymous_output_39 | n/a |
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_anonymous_output_40 | _anonymous_output_40 | n/a |
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mycpptraj_rms.dat | mycpptraj_rms.dat | n/a |
|
_anonymous_output_41 | _anonymous_output_41 | n/a |
|
mycpptraj_rgyr.dat | mycpptraj_rgyr.dat | n/a |
|
mycpptraj_image.trr | mycpptraj_image.trr | n/a |
|
Version History
Version 3 (latest) Created 3rd May 2023 at 14:52 by Genís Bayarri
Update to BioBB 4.0.*
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Version-3
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Version 2 Created 23rd Nov 2022 at 08:43 by Genís Bayarri
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Version-2
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Version 1 (earliest) Created 25th Mar 2022 at 11:42 by Genís Bayarri
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Creators and Submitter
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Citation
Hospital, A., & Bayarri, G. (2023). Galaxy Amber Protein Ligand Complex MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.298.3
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Views: 4269 Downloads: 779 Runs: 0
Created: 25th Mar 2022 at 11:42
Last updated: 3rd May 2023 at 14:52
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