Workflow Type: Galaxy
Frozen
This is a Galaxy workflow for performing molecular dynamics simulations and analysis with coronavirus helicases bound to a ligand/drug molecule. The associated input files can be found at: https://zenodo.org/records/7492987. The associated output files can be found at: https://zenodo.org/records/7851000.
Inputs
ID | Name | Description | Type |
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ligand frcmod file | #main/ligand frcmod file | n/a |
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ligand mol2 file | #main/ligand mol2 file | n/a |
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protein-ligand complex pdb file | #main/protein-ligand complex pdb file | n/a |
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specialized FF frcmod file | #main/specialized FF frcmod file | n/a |
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specialized FF prep file | #main/specialized FF prep file | n/a |
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Steps
ID | Name | Description |
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5 | GROMACS copy file | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_get_builtin_file/gmx_get_builtin_file/2022+galaxy0 |
6 | GROMACS copy file | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_get_builtin_file/gmx_get_builtin_file/2022+galaxy0 |
7 | Build tLEaP | toolshed.g2.bx.psu.edu/repos/chemteam/tleap/tleap/21.10+galaxy0 |
8 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
9 | extract topology file | __EXTRACT_DATASET__ |
10 | extract coordinate file | __EXTRACT_DATASET__ |
11 | Convert Amber topology and coordinate files to GROMACS format | toolshed.g2.bx.psu.edu/repos/chemteam/acpype_amber2gromacs/acpype_Amber2Gromacs/21.10+galaxy0 |
12 | Adding New Topology Information | toolshed.g2.bx.psu.edu/repos/chemteam/gromacs_modify_topology/gromacs_modify_topology/0+galaxy0 |
13 | GROMACS structure configuration | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2022+galaxy0 |
14 | GROMACS solvation and adding ions | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2022+galaxy0 |
15 | Create GROMACS index files | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_makendx/gmx_makendx/2022+galaxy0 |
16 | Create GROMACS position restraints files | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_restraints/gmx_restraints/2022+galaxy0 |
17 | Adding New Topology Information | toolshed.g2.bx.psu.edu/repos/chemteam/gromacs_modify_topology/gromacs_modify_topology/0+galaxy0 |
18 | GROMACS energy minimization | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2022+galaxy0 |
19 | NVT | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0 |
20 | NPT | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0 |
21 | prod1 | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0 |
22 | prod2 | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0 |
23 | prod3 | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0 |
24 | prod4 | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0 |
25 | Modify/convert and concatate GROMACS trajectories | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_trj/gmx_trj/2022+galaxy2 |
26 | Modify/convert and concatate GROMACS trajectories | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_trj/gmx_trj/2022+galaxy2 |
27 | Modify/convert and concatate GROMACS trajectories | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_trj/gmx_trj/2022+galaxy2 |
28 | GROMACS RMSD calculation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_rmsd/gmx_rmsd/2022+galaxy0 |
29 | GROMACS RMSF calculation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_rmsf/gmx_rmsf/2022+galaxy0 |
Outputs
ID | Name | Description | Type |
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GROMACS calculation of RMSD on input dataset(s) | #main/GROMACS calculation of RMSD on input dataset(s) | n/a |
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GROMACS calculation of RMSF on input dataset(s) | #main/GROMACS calculation of RMSF on input dataset(s) | n/a |
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_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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_anonymous_output_10 | #main/_anonymous_output_10 | n/a |
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_anonymous_output_11 | #main/_anonymous_output_11 | n/a |
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_anonymous_output_12 | #main/_anonymous_output_12 | n/a |
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_anonymous_output_13 | #main/_anonymous_output_13 | n/a |
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_anonymous_output_14 | #main/_anonymous_output_14 | n/a |
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_anonymous_output_15 | #main/_anonymous_output_15 | n/a |
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_anonymous_output_16 | #main/_anonymous_output_16 | n/a |
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_anonymous_output_17 | #main/_anonymous_output_17 | n/a |
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_anonymous_output_18 | #main/_anonymous_output_18 | n/a |
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_anonymous_output_19 | #main/_anonymous_output_19 | n/a |
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_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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_anonymous_output_20 | #main/_anonymous_output_20 | n/a |
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_anonymous_output_21 | #main/_anonymous_output_21 | n/a |
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_anonymous_output_22 | #main/_anonymous_output_22 | n/a |
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_anonymous_output_23 | #main/_anonymous_output_23 | n/a |
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_anonymous_output_24 | #main/_anonymous_output_24 | n/a |
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_anonymous_output_25 | #main/_anonymous_output_25 | n/a |
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_anonymous_output_26 | #main/_anonymous_output_26 | n/a |
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_anonymous_output_27 | #main/_anonymous_output_27 | n/a |
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_anonymous_output_28 | #main/_anonymous_output_28 | n/a |
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_anonymous_output_29 | #main/_anonymous_output_29 | n/a |
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_anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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_anonymous_output_30 | #main/_anonymous_output_30 | n/a |
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_anonymous_output_31 | #main/_anonymous_output_31 | n/a |
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_anonymous_output_32 | #main/_anonymous_output_32 | n/a |
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_anonymous_output_33 | #main/_anonymous_output_33 | n/a |
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_anonymous_output_34 | #main/_anonymous_output_34 | n/a |
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_anonymous_output_35 | #main/_anonymous_output_35 | n/a |
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_anonymous_output_36 | #main/_anonymous_output_36 | n/a |
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_anonymous_output_37 | #main/_anonymous_output_37 | n/a |
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_anonymous_output_38 | #main/_anonymous_output_38 | n/a |
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_anonymous_output_39 | #main/_anonymous_output_39 | n/a |
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_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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_anonymous_output_40 | #main/_anonymous_output_40 | n/a |
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_anonymous_output_41 | #main/_anonymous_output_41 | n/a |
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_anonymous_output_42 | #main/_anonymous_output_42 | n/a |
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_anonymous_output_43 | #main/_anonymous_output_43 | n/a |
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_anonymous_output_44 | #main/_anonymous_output_44 | n/a |
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_anonymous_output_45 | #main/_anonymous_output_45 | n/a |
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_anonymous_output_46 | #main/_anonymous_output_46 | n/a |
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_anonymous_output_47 | #main/_anonymous_output_47 | n/a |
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_anonymous_output_48 | #main/_anonymous_output_48 | n/a |
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_anonymous_output_49 | #main/_anonymous_output_49 | n/a |
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_anonymous_output_5 | #main/_anonymous_output_5 | n/a |
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_anonymous_output_50 | #main/_anonymous_output_50 | n/a |
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_anonymous_output_51 | #main/_anonymous_output_51 | n/a |
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_anonymous_output_52 | #main/_anonymous_output_52 | n/a |
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_anonymous_output_53 | #main/_anonymous_output_53 | n/a |
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_anonymous_output_54 | #main/_anonymous_output_54 | n/a |
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_anonymous_output_6 | #main/_anonymous_output_6 | n/a |
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_anonymous_output_7 | #main/_anonymous_output_7 | n/a |
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_anonymous_output_8 | #main/_anonymous_output_8 | n/a |
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_anonymous_output_9 | #main/_anonymous_output_9 | n/a |
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input dataset(s) (extracted element) | #main/input dataset(s) (extracted element) | n/a |
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Version History
Version 1 (earliest) Created 16th Feb 2024 at 19:04 by Bryan Raubenolt
Initial commit
Frozen
Version-1
7fcea04
Creators and Submitter
Creator
Submitter
Citation
Raubenolt, B. (2024). coronavirushelicase_proteindrugcomplex. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.763.1
Activity
Views: 2126 Downloads: 464 Runs: 0
Created: 16th Feb 2024 at 19:04
Last updated: 29th Feb 2024 at 16:39
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