Astrocyte PDB2PQR Workflow Package

This is the PDB2PQR workflow for Astrocyte. It runs alphafold/2.0.1 to transform the pdb file to a pqr file.

The Workflow

The workflow workflow/main.nf has two processes:

• Collect the input parameters
• Convert the parameters to pdb2pqr required formats and run pdb2pqr

Parameters

• pdb PDB files

• forcefield The forcefield to use. (default: PARSE)

• dropwater Drop waters before processing biomolecule. (default: False)

• titrationstate Method used to calculate titration states. If a titration state method is selected, titratable residue charge states will be set by the pH value supplied by --with_ph (default: None)

• withpH pH values to use when applying the results of the selected pH calculation method. (default: 7.0)

Questions

If you have any questions about this workflow, or Astrocyte in general, please contact the BioHPC team via biohpc-help@utsouthwestern.edu