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.

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 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.top myleap_gen_top.top n/a
  • File
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
  • File
myleap_add_ions.parmtop myleap_add_ions.parmtop n/a
  • File
myleap_add_ions.pdb myleap_add_ions.pdb n/a
  • File
myleap_add_ions.crd myleap_add_ions.crd n/a
  • File
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.mdinfo mysander_mdrun.mdinfo n/a
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mysander_mdrun.ncrst mysander_mdrun.ncrst n/a
  • File
mysander_mdrun.nc mysander_mdrun.nc n/a
  • File
mysander_mdrun.cprst mysander_mdrun.cprst 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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_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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_anonymous_output_9 _anonymous_output_9 n/a
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_anonymous_output_10 _anonymous_output_10 n/a
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_anonymous_output_11 _anonymous_output_11 n/a
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_anonymous_output_12 _anonymous_output_12 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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_anonymous_output_14 _anonymous_output_14 n/a
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_anonymous_output_15 _anonymous_output_15 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
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_anonymous_output_34 _anonymous_output_34 n/a
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_anonymous_output_35 _anonymous_output_35 n/a
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_anonymous_output_36 _anonymous_output_36 n/a
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_anonymous_output_52 _anonymous_output_52 n/a
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_anonymous_output_57 _anonymous_output_57 n/a
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_anonymous_output_58 _anonymous_output_58 n/a
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_anonymous_output_68 _anonymous_output_68 n/a
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Version History

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

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Frozen Version-2 5650af6

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

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Frozen Version-1 8592492
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Citation
Hospital, A., & Bayarri, G. (2022). Galaxy ABC MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.299.2
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Created: 29th Mar 2022 at 11:43

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