Galaxy ABC MD Setup tutorial

View on GitHub Download RO-Crate Run on Galaxy
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.

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
  • File
myleap_gen_top.pdb myleap_gen_top.pdb n/a
  • File
myleap_solvate.crd myleap_solvate.crd n/a
  • File
myleap_solvate.parmtop myleap_solvate.parmtop n/a
  • File
myleap_solvate.pdb myleap_solvate.pdb 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.log mysander_mdrun.log n/a
  • File
mysander_mdrun.cpout mysander_mdrun.cpout n/a
  • File
mysander_mdrun.cprst mysander_mdrun.cprst n/a
  • File
mysander_mdrun.nc mysander_mdrun.nc n/a
  • File
mysander_mdrun.ncrst mysander_mdrun.ncrst n/a
  • File
mysander_mdrun.mdinfo mysander_mdrun.mdinfo n/a
  • File
myprocess_minout.dat myprocess_minout.dat n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
myprocess_mdout.dat myprocess_mdout.dat n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
  • File
_anonymous_output_13 _anonymous_output_13 n/a
  • File
_anonymous_output_14 _anonymous_output_14 n/a
  • File
_anonymous_output_15 _anonymous_output_15 n/a
  • File
_anonymous_output_16 _anonymous_output_16 n/a
  • File
_anonymous_output_17 _anonymous_output_17 n/a
  • File
_anonymous_output_18 _anonymous_output_18 n/a
  • File
_anonymous_output_19 _anonymous_output_19 n/a
  • File
_anonymous_output_20 _anonymous_output_20 n/a
  • File
_anonymous_output_21 _anonymous_output_21 n/a
  • File
_anonymous_output_22 _anonymous_output_22 n/a
  • File
_anonymous_output_23 _anonymous_output_23 n/a
  • File
_anonymous_output_24 _anonymous_output_24 n/a
  • File
_anonymous_output_25 _anonymous_output_25 n/a
  • File
_anonymous_output_26 _anonymous_output_26 n/a
  • File
_anonymous_output_27 _anonymous_output_27 n/a
  • File
_anonymous_output_28 _anonymous_output_28 n/a
  • File
_anonymous_output_29 _anonymous_output_29 n/a
  • File
_anonymous_output_30 _anonymous_output_30 n/a
  • File
_anonymous_output_31 _anonymous_output_31 n/a
  • File
_anonymous_output_32 _anonymous_output_32 n/a
  • File
_anonymous_output_33 _anonymous_output_33 n/a
  • File
_anonymous_output_34 _anonymous_output_34 n/a
  • File
_anonymous_output_35 _anonymous_output_35 n/a
  • File
_anonymous_output_36 _anonymous_output_36 n/a
  • File
_anonymous_output_37 _anonymous_output_37 n/a
  • File
_anonymous_output_38 _anonymous_output_38 n/a
  • File
_anonymous_output_39 _anonymous_output_39 n/a
  • File
_anonymous_output_40 _anonymous_output_40 n/a
  • File
_anonymous_output_41 _anonymous_output_41 n/a
  • File
_anonymous_output_42 _anonymous_output_42 n/a
  • File
_anonymous_output_43 _anonymous_output_43 n/a
  • File
_anonymous_output_44 _anonymous_output_44 n/a
  • File
_anonymous_output_45 _anonymous_output_45 n/a
  • File
_anonymous_output_46 _anonymous_output_46 n/a
  • File
_anonymous_output_47 _anonymous_output_47 n/a
  • File
_anonymous_output_48 _anonymous_output_48 n/a
  • File
_anonymous_output_49 _anonymous_output_49 n/a
  • File
_anonymous_output_50 _anonymous_output_50 n/a
  • File
_anonymous_output_51 _anonymous_output_51 n/a
  • File
_anonymous_output_52 _anonymous_output_52 n/a
  • File
_anonymous_output_53 _anonymous_output_53 n/a
  • File
_anonymous_output_54 _anonymous_output_54 n/a
  • File
_anonymous_output_55 _anonymous_output_55 n/a
  • File
_anonymous_output_56 _anonymous_output_56 n/a
  • File
_anonymous_output_57 _anonymous_output_57 n/a
  • File
_anonymous_output_58 _anonymous_output_58 n/a
  • File
_anonymous_output_59 _anonymous_output_59 n/a
  • File
_anonymous_output_60 _anonymous_output_60 n/a
  • File
_anonymous_output_61 _anonymous_output_61 n/a
  • File
_anonymous_output_62 _anonymous_output_62 n/a
  • File
_anonymous_output_63 _anonymous_output_63 n/a
  • File
_anonymous_output_64 _anonymous_output_64 n/a
  • File
_anonymous_output_65 _anonymous_output_65 n/a
  • File
_anonymous_output_66 _anonymous_output_66 n/a
  • File
_anonymous_output_67 _anonymous_output_67 n/a
  • File
_anonymous_output_68 _anonymous_output_68 n/a
  • File

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
Creators
Submitter
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: 4430   Downloads: 712   Runs: 0

Created: 29th Mar 2022 at 11:43

Last updated: 3rd May 2023 at 14:54

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 164 KB
Powered by
 (v.1.16.0-main)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH