How to prepare input PDB file (not from PDB database) for MD simulation in BioExcel Building Blocks?

BioBB
1

How to prepare input PDB file (not from PDB database) for MD simulation? Please guide me.
I am following tutorial on “Protein MD Setup tutorial using BioExcel Building Blocks (biobb)”: Protein MD Setup tutorial - BioExcel Building Blocks

2

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-