Galaxy Amber Protein MD Setup tutorial

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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/297?version=3

DOI: 10.48546/workflowhub.workflow.297.3

Steps

ID Name Description
0 Pdb biobb_io_pdb_ext
1 Pdb4amberRun biobb_amber_pdb4amber_run_ext
2 LeapGenTop biobb_amber_leap_gen_top_ext
3 SanderMdrun MinH biobb_amber_sander_mdrun_ext
4 SanderMdrun MinSys biobb_amber_sander_mdrun_ext
5 ProcessMinout biobb_amber_process_minout_ext
6 AmberToPdb biobb_amber_amber_to_pdb_ext
7 ProcessMinout biobb_amber_process_minout_ext
8 LeapSolvate biobb_amber_leap_solvate_ext
9 LeapAddIons biobb_amber_leap_add_ions_ext
10 SanderMdrun Energy Min biobb_amber_sander_mdrun_ext
11 ProcessMinout biobb_amber_process_minout_ext
12 SanderMdrun Warm Up biobb_amber_sander_mdrun_ext
13 ProcessMdout biobb_amber_process_mdout_ext
14 SanderMdrun NVT biobb_amber_sander_mdrun_ext
15 ProcessMdout biobb_amber_process_mdout_ext
16 SanderMdrun NPT biobb_amber_sander_mdrun_ext
17 ProcessMdout biobb_amber_process_mdout_ext
18 SanderMdrun Free biobb_amber_sander_mdrun_ext
19 CpptrajRms First biobb_analysis_cpptraj_rms_ext
20 CpptrajRms Exp biobb_analysis_cpptraj_rms_ext
21 CpptrajRgyr biobb_analysis_cpptraj_rgyr_ext
22 CpptrajImage biobb_analysis_cpptraj_image_ext

Outputs

ID Name Description Type
mypdb.pdb mypdb.pdb n/a
  • File
mypdb4amber_run.pdb mypdb4amber_run.pdb n/a
  • File
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
mysander_mdrun.rst mysander_mdrun.rst n/a
  • File
mysander_mdrun.trj mysander_mdrun.trj n/a
  • File
mysander_mdrun.cpout mysander_mdrun.cpout n/a
  • File
mysander_mdrun.cprst mysander_mdrun.cprst n/a
  • File
mysander_mdrun.mdinfo mysander_mdrun.mdinfo n/a
  • File
mysander_mdrun.log mysander_mdrun.log 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_minout.dat myprocess_minout.dat n/a
  • File
myamber_to_pdb.pdb myamber_to_pdb.pdb n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
myleap_solvate.top myleap_solvate.top n/a
  • File
myleap_solvate.crd myleap_solvate.crd n/a
  • File
myleap_solvate.pdb myleap_solvate.pdb n/a
  • File
myleap_add_ions.pdb myleap_add_ions.pdb n/a
  • File
myleap_add_ions.top myleap_add_ions.top n/a
  • File
myleap_add_ions.crd myleap_add_ions.crd 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
myprocess_mdout.dat myprocess_mdout.dat 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
mysander_mdrun.netcdf mysander_mdrun.netcdf n/a
  • File
_anonymous_output_38 _anonymous_output_38 n/a
  • File
_anonymous_output_39 _anonymous_output_39 n/a
  • File
mycpptraj_rms.dat mycpptraj_rms.dat n/a
  • File
_anonymous_output_40 _anonymous_output_40 n/a
  • File
mycpptraj_rgyr.dat mycpptraj_rgyr.dat n/a
  • File
mycpptraj_image.trr mycpptraj_image.trr n/a
  • File

Version History

Version 3 (latest) Created 3rd May 2023 at 14:49 by Genís Bayarri

Update to BioBB 4.0.*


Frozen Version-3 69dcddd

Version 2 Created 23rd Nov 2022 at 13:28 by Genís Bayarri

No revision comments

Frozen Version-2 4f14959

Version 1 (earliest) Created 25th Mar 2022 at 10:10 by Genís Bayarri

Initial commit


Frozen Version-1 77500af
help Creators and Submitter
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Tutorial
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Citation
Hospital, A., & Bayarri, G. (2023). Galaxy Amber Protein MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.297.3
License
Apache License 2.0
Activity

Views: 4812   Downloads: 881   Runs: 0

Created: 25th Mar 2022 at 10:10

Last updated: 3rd May 2023 at 14:50

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