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

**URL:** https://ask.bioexcel.eu/t/how-to-prepare-input-pdb-file-not-from-pdb-database-for-md-simulation-in-bioexcel-building-blocks/3681
**Category:** BioBB
**Created:** [April 18, 2022, 5:24pm UTC](https://ask.bioexcel.eu/t/how-to-prepare-input-pdb-file-not-from-pdb-database-for-md-simulation-in-bioexcel-building-blocks/3681 "2022-04-18T17:24:52Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![Hamza](https://avatars.discourse-cdn.com/v4/letter/h/a88e57/32.png) [@Hamza](https://ask.bioexcel.eu/u/Hamza)
#### Post date: [April 18, 2022, 5:24pm UTC](https://ask.bioexcel.eu/t/how-to-prepare-input-pdb-file-not-from-pdb-database-for-md-simulation-in-bioexcel-building-blocks/3681/1 "2022-04-18T17:24:52Z")

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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](https://mmb.irbbarcelona.org/biobb/availability/tutorials/md_setup)

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### Author: ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)
#### Post date: [April 25, 2022, 1:24pm UTC](https://ask.bioexcel.eu/t/how-to-prepare-input-pdb-file-not-from-pdb-database-for-md-simulation-in-bioexcel-building-blocks/3681/2 "2022-04-25T13:24:51Z")

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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:

```auto
# 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-