Galaxy Amber Protein Ligand Complex 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/298?version=3

DOI: 10.48546/workflowhub.workflow.298.3

Steps

ID Name Description
0 Pdb biobb_io_pdb_ext
1 RemovePdbWater biobb_structure_utils_remove_pdb_water_ext
2 RemoveLigand PO4 biobb_structure_utils_remove_ligand_ext
3 RemoveLigand BME biobb_structure_utils_remove_ligand_ext
4 Pdb4amberRun biobb_amber_pdb4amber_run_ext
5 ExtractHeteroatoms biobb_structure_utils_extract_heteroatoms_ext
6 ReduceAddHydrogens biobb_chemistry_reduce_add_hydrogens_ext
7 BabelMinimize biobb_chemistry_babel_minimize_ext
8 AcpypeParamsAc biobb_chemistry_acpype_params_ac_ext
9 LeapGenTop biobb_amber_leap_gen_top_ext
10 SanderMdrun MinH biobb_amber_sander_mdrun_ext
11 ProcessMinout biobb_amber_process_minout_ext
12 SanderMdrun MinSys biobb_amber_sander_mdrun_ext
13 AmberToPdb biobb_amber_amber_to_pdb_ext
14 ProcessMinout biobb_amber_process_minout_ext
15 LeapSolvate biobb_amber_leap_solvate_ext
16 LeapAddIons biobb_amber_leap_add_ions_ext
17 SanderMdrun Energy Min biobb_amber_sander_mdrun_ext
18 ProcessMinout biobb_amber_process_minout_ext
19 SanderMdrun Warm Up biobb_amber_sander_mdrun_ext
20 ProcessMdout biobb_amber_process_mdout_ext
21 SanderMdrun NVT biobb_amber_sander_mdrun_ext
22 ProcessMdout biobb_amber_process_mdout_ext
23 SanderMdrun NPT biobb_amber_sander_mdrun_ext
24 ProcessMdout biobb_amber_process_mdout_ext
25 SanderMdrun Free biobb_amber_sander_mdrun_ext
26 CpptrajRms First biobb_analysis_cpptraj_rms_ext
27 CpptrajRms Exp biobb_analysis_cpptraj_rms_ext
28 CpptrajRgyr biobb_analysis_cpptraj_rgyr_ext
29 CpptrajImage biobb_analysis_cpptraj_image_ext

Outputs

ID Name Description Type
mypdb.pdb mypdb.pdb n/a
  • File
myremove_pdb_water.pdb myremove_pdb_water.pdb n/a
  • File
myremove_ligand.pdb myremove_ligand.pdb n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
mypdb4amber_run.pdb mypdb4amber_run.pdb n/a
  • File
myextract_heteroatoms.pdb myextract_heteroatoms.pdb n/a
  • File
myreduce_add_hydrogens.pdb myreduce_add_hydrogens.pdb n/a
  • File
mybabel_minimize.mol2 mybabel_minimize.mol2 n/a
  • File
myacpype_params_ac.prmtop myacpype_params_ac.prmtop n/a
  • File
myacpype_params_ac.inpcrd myacpype_params_ac.inpcrd n/a
  • File
myacpype_params_ac.frcmod myacpype_params_ac.frcmod n/a
  • File
myacpype_params_ac.lib myacpype_params_ac.lib n/a
  • File
myleap_gen_top.pdb myleap_gen_top.pdb n/a
  • File
myleap_gen_top.top myleap_gen_top.top n/a
  • File
myleap_gen_top.crd myleap_gen_top.crd n/a
  • File
mysander_mdrun.log mysander_mdrun.log n/a
  • File
mysander_mdrun.rst mysander_mdrun.rst n/a
  • File
mysander_mdrun.cpout mysander_mdrun.cpout n/a
  • File
mysander_mdrun.mdinfo mysander_mdrun.mdinfo n/a
  • File
mysander_mdrun.cprst mysander_mdrun.cprst n/a
  • File
mysander_mdrun.trj mysander_mdrun.trj n/a
  • File
myprocess_minout.dat myprocess_minout.dat 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
_anonymous_output_7 _anonymous_output_7 n/a
  • File
myamber_to_pdb.pdb myamber_to_pdb.pdb n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
myleap_solvate.pdb myleap_solvate.pdb n/a
  • File
myleap_solvate.parmtop myleap_solvate.parmtop n/a
  • File
myleap_solvate.crd myleap_solvate.crd 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
myleap_add_ions.parmtop myleap_add_ions.parmtop 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
myprocess_mdout.dat myprocess_mdout.dat 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
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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
  • File
_anonymous_output_35 _anonymous_output_35 n/a
  • File
_anonymous_output_36 _anonymous_output_36 n/a
  • File
mysander_mdrun.netcdf mysander_mdrun.netcdf 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
mycpptraj_rms.dat mycpptraj_rms.dat n/a
  • File
_anonymous_output_41 _anonymous_output_41 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 14:52 by Genís Bayarri

Update to BioBB 4.0.*


Frozen Version-3 01562ec

Version 2 Created 23rd Nov 2022 at 08:43 by Genís Bayarri

No revision comments

Frozen Version-2 a4afa1e

Version 1 (earliest) Created 25th Mar 2022 at 11:42 by Genís Bayarri

Initial commit


Frozen Version-1 000da69
help Creators and Submitter
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Citation
Hospital, A., & Bayarri, G. (2023). Galaxy Amber Protein Ligand Complex MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.298.3
License
Apache License 2.0
Activity

Views: 4757   Downloads: 934   Runs: 0

Created: 25th Mar 2022 at 11:42

Last updated: 3rd May 2023 at 14:52

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