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).
- (c) 2015-2022 Barcelona Supercomputing Center
- (c) 2015-2022 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Steps
ID | Name | Description |
---|---|---|
0 | LeapGenTop | biobb_amber_leap_gen_top_ext |
1 | LeapSolvate | biobb_amber_leap_solvate_ext |
2 | LeapAddIons | biobb_amber_leap_add_ions_ext |
3 | ParmedHmassrepartition | biobb_amber_parmed_hmassrepartition_ext |
4 | CpptrajRandomizeIons | biobb_amber_cpptraj_randomize_ions_ext |
5 | SanderMdrun Step1 | biobb_amber_sander_mdrun_ext |
6 | SanderMdrun Step2 NVT | biobb_amber_sander_mdrun_ext |
7 | ProcessMinout | biobb_amber_process_minout_ext |
8 | SanderMdrun Step3 | biobb_amber_sander_mdrun_ext |
9 | ProcessMdout | biobb_amber_process_mdout_ext |
10 | SanderMdrun Step4 | biobb_amber_sander_mdrun_ext |
11 | ProcessMinout | biobb_amber_process_minout_ext |
12 | SanderMdrun Step5 | biobb_amber_sander_mdrun_ext |
13 | ProcessMinout | biobb_amber_process_minout_ext |
14 | SanderMdrun Step6 NPT | biobb_amber_sander_mdrun_ext |
15 | ProcessMinout | biobb_amber_process_minout_ext |
16 | SanderMdrun Step7 NPT | biobb_amber_sander_mdrun_ext |
17 | ProcessMdout | biobb_amber_process_mdout_ext |
18 | SanderMdrun Step8 NPT | biobb_amber_sander_mdrun_ext |
19 | ProcessMdout | biobb_amber_process_mdout_ext |
20 | ProcessMdout | biobb_amber_process_mdout_ext |
21 | SanderMdrun Step9 NPT | biobb_amber_sander_mdrun_ext |
22 | ProcessMdout | biobb_amber_process_mdout_ext |
23 | SanderMdrun Step10 NPT | biobb_amber_sander_mdrun_ext |
24 | ProcessMdout | biobb_amber_process_mdout_ext |
25 | SanderMdrun Free | biobb_amber_sander_mdrun_ext |
Outputs
ID | Name | Description | Type |
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myleap_gen_top.top | myleap_gen_top.top | n/a |
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myleap_gen_top.pdb | myleap_gen_top.pdb | n/a |
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myleap_gen_top.crd | myleap_gen_top.crd | n/a |
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myleap_solvate.crd | myleap_solvate.crd | n/a |
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myleap_solvate.pdb | myleap_solvate.pdb | n/a |
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myleap_solvate.parmtop | myleap_solvate.parmtop | n/a |
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myleap_add_ions.parmtop | myleap_add_ions.parmtop | n/a |
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myleap_add_ions.pdb | myleap_add_ions.pdb | n/a |
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myleap_add_ions.crd | myleap_add_ions.crd | n/a |
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myparmed_hmassrepartition.top | myparmed_hmassrepartition.top | n/a |
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mycpptraj_randomize_ions.crd | mycpptraj_randomize_ions.crd | n/a |
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mycpptraj_randomize_ions.pdb | mycpptraj_randomize_ions.pdb | n/a |
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mysander_mdrun.mdinfo | mysander_mdrun.mdinfo | n/a |
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mysander_mdrun.ncrst | mysander_mdrun.ncrst | n/a |
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mysander_mdrun.nc | mysander_mdrun.nc | n/a |
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mysander_mdrun.cprst | mysander_mdrun.cprst | n/a |
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mysander_mdrun.log | mysander_mdrun.log | n/a |
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mysander_mdrun.cpout | mysander_mdrun.cpout | n/a |
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_anonymous_output_1 | _anonymous_output_1 | n/a |
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_anonymous_output_2 | _anonymous_output_2 | n/a |
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_anonymous_output_3 | _anonymous_output_3 | n/a |
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_anonymous_output_4 | _anonymous_output_4 | n/a |
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_anonymous_output_5 | _anonymous_output_5 | n/a |
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_anonymous_output_6 | _anonymous_output_6 | n/a |
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myprocess_minout.dat | myprocess_minout.dat | n/a |
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_anonymous_output_7 | _anonymous_output_7 | n/a |
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_anonymous_output_8 | _anonymous_output_8 | n/a |
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myprocess_mdout.dat | myprocess_mdout.dat | n/a |
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_anonymous_output_13 | _anonymous_output_13 | n/a |
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Version History
Version 3 (latest) Created 3rd May 2023 at 14:54 by Genís Bayarri
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Version 2 Created 23rd Nov 2022 at 09:03 by Genís Bayarri
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Version 1 (earliest) Created 29th Mar 2022 at 11:43 by Genís Bayarri
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Citation
Hospital, A., & Bayarri, G. (2022). Galaxy ABC MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.299.1
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Views: 4620 Downloads: 777 Runs: 0
Created: 29th Mar 2022 at 11:43
Last updated: 3rd May 2023 at 14:54
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