coronavirushelicase_proteindrugcomplex
Version 1

Workflow Type: Galaxy

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
ligand frcmod file #main/ligand frcmod file n/a
  • File
ligand mol2 file #main/ligand mol2 file n/a
  • File
protein-ligand complex pdb file #main/protein-ligand complex pdb file n/a
  • File
specialized FF frcmod file #main/specialized FF frcmod file n/a
  • File
specialized FF prep file #main/specialized FF prep file n/a
  • File

Steps

ID Name Description
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
GROMACS calculation of RMSD on input dataset(s) #main/GROMACS calculation of RMSD on input dataset(s) n/a
  • File
GROMACS calculation of RMSF on input dataset(s) #main/GROMACS calculation of RMSF on input dataset(s) n/a
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_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
  • File

Version History

Version 1 (earliest) Created 16th Feb 2024 at 19:04 by Bryan Raubenolt

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Frozen Version-1 7fcea04
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Citation
Raubenolt, B. (2024). coronavirushelicase_proteindrugcomplex. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.763.1
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Views: 968   Downloads: 209

Created: 16th Feb 2024 at 19:04

Last updated: 29th Feb 2024 at 16:39

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