Introduction

in this tutorial, we show some common functions included in PENSA, using trajectories of a G protein-coupled receptor (GPCR). We retrieve the molecular dynamics trajectories for this tutorial from GPCRmd, an online platform for collection and curation of GPCR simulations. It is described in more detail here.

The example system is the mu-opioid receptor (mOR), once in its apo form and once bound to the ligand BU72. The structure of this GPCR has been reported by Huang et al (2015). We are going to compare the structural ensembles of the receptor in these two conditions.

This tutorial assumes that you can download the trajectories (see below). If you can’t, you can use any other system you have available and adapt the file names and residue selections accordingly.

Download

We only need to import the module “os” and PENSA’s predefined function to download GPCRmd trajectories here.

import os
from pensa.preprocessing import download_from_gpcrmd

File names usually have to be looked up on the GPCRmd website but we have done this already. Just execute the following to obtain the example for this tutorial:

# Define where to save the GPCRmd files
root_dir = './mor-data'
# Define which files to download
md_files = ['11427_dyn_151.psf','11426_dyn_151.pdb', # MOR-apo
            '11423_trj_151.xtc','11424_trj_151.xtc','11425_trj_151.xtc',
            '11580_dyn_169.psf','11579_dyn_169.pdb', # MOR-BU72
            '11576_trj_169.xtc','11577_trj_169.xtc','11578_trj_169.xtc']
# Download all the files that do not exist yet
for file in md_files:
    if not os.path.exists(os.path.join(root_dir,file)):
        download_from_gpcrmd(file,root_dir)