Galaxy ABC MD Setup tutorial

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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.

SEEK ID: https://workflowhub.eu/workflows/299?version=3

DOI: 10.48546/workflowhub.workflow.299.3

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 ProcessMinout biobb_amber_process_minout_ext
7 SanderMdrun Step2 NVT biobb_amber_sander_mdrun_ext
8 ProcessMdout biobb_amber_process_mdout_ext
9 SanderMdrun Step3 biobb_amber_sander_mdrun_ext
10 ProcessMinout biobb_amber_process_minout_ext
11 SanderMdrun Step4 biobb_amber_sander_mdrun_ext
12 ProcessMinout biobb_amber_process_minout_ext
13 SanderMdrun Step5 biobb_amber_sander_mdrun_ext
14 SanderMdrun Step6 NPT biobb_amber_sander_mdrun_ext
15 ProcessMinout biobb_amber_process_minout_ext
16 ProcessMdout biobb_amber_process_mdout_ext
17 SanderMdrun Step7 NPT biobb_amber_sander_mdrun_ext
18 ProcessMdout biobb_amber_process_mdout_ext
19 SanderMdrun Step8 NPT biobb_amber_sander_mdrun_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
myleap_gen_top.crd myleap_gen_top.crd n/a
  • File
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_solvate.crd myleap_solvate.crd n/a
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myleap_solvate.parmtop myleap_solvate.parmtop n/a
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myleap_solvate.pdb myleap_solvate.pdb 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
  • File
mycpptraj_randomize_ions.crd mycpptraj_randomize_ions.crd n/a
  • File
mycpptraj_randomize_ions.pdb mycpptraj_randomize_ions.pdb n/a
  • File
mysander_mdrun.log mysander_mdrun.log n/a
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mysander_mdrun.cpout mysander_mdrun.cpout n/a
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mysander_mdrun.cprst mysander_mdrun.cprst n/a
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mysander_mdrun.nc mysander_mdrun.nc n/a
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mysander_mdrun.ncrst mysander_mdrun.ncrst n/a
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mysander_mdrun.mdinfo mysander_mdrun.mdinfo n/a
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myprocess_minout.dat myprocess_minout.dat 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_mdout.dat myprocess_mdout.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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Version History

Version 3 (latest) Created 3rd May 2023 at 14:54 by Genís Bayarri

No revision comments

Frozen Version-3 4a10ff4

Version 2 Created 23rd Nov 2022 at 09:03 by Genís Bayarri

No revision comments

Frozen Version-2 5650af6

Version 1 (earliest) Created 29th Mar 2022 at 11:43 by Genís Bayarri

Initial commit


Frozen Version-1 8592492
help Creators and Submitter
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Discussion Channels
BioExcel Workflows
Galaxy
Documentation
Citation
Hospital, A., & Bayarri, G. (2023). Galaxy ABC MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.299.3
License
Apache License 2.0
Activity

Views: 4414   Downloads: 707   Runs: 0

Created: 29th Mar 2022 at 11:43

Last updated: 3rd May 2023 at 14:54

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