How to prepare input PDB file (not from PDB database) for MD simulation?

Please help me on how to prepare input PDB file (not from PDB database) for MD simulation?
This tutorial is for protein structures available in PDB database: Protein MD Setup tutorial - BioExcel Building Blocks

Hi Hamza,

sorry for the late reply.

You should comment the Jupyter cell where a PDB structure is downloaded from the PDB database and substitute it for the structure in your file system.

As an example:

# Downloading desired PDB file 
# Import module
#from biobb_io.api.pdb import pdb

# Create properties dict and inputs/outputs
#downloaded_pdb = pdbCode+'.pdb'
#prop = {
#    'pdb_code': pdbCode
#}

#Create and launch bb
#pdb(output_pdb_path=downloaded_pdb,
#    properties=prop)

downloaded_pdb = "/Path/to/your/file/complex_H.pdb"

Hope it helps!

-Adam-