Galaxy | BRIDGE | Accessible Workflow | HTMD simulation with collections

HTMD simulation with collections

Step	Annotation
Step 1: Get PDB file PDB accession code 6hhr
Step 2: Input dataset SDF file with (docked) ligands select at runtime
Step 3: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1'
Step 4: Compound conversion Molecular input file Output dataset 'output' from step 2 Output format Sybyl Mol2 format (mol2) Output ignores residue information for ligands? False Generate 2D coordinates False Generate 3D coordinates False Delete hydrogen atoms, make all hydrogens implicit False Add hydrogens appropriate for pH 7.0 Convert dative bonds False Append the specified text after each molecule title Empty. Uniqueness according to No unique filter
Step 5: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.4'
Step 6: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/19.11'
Step 7: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0'
Step 8: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4'
Step 9: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.4'
Step 10: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2019.1.4'
Step 11: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1'
Step 12: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1'
Step 13: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1'

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