Complex Formation Tutorial

Welcome to the 2nd tutorial of eSBMTools. In this tutorial we'll see how to merge 2 proteins and simulate the resulting complex formed. This example merges the proteins '1IXM' & '1PEY' to form the protein '1F51'.

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→ To start the tutorial, first run the python script present in the folder using the following command:

            $> python buildComplex.py

This script generates a number of files:

        -start1.gro         -start1.top
        -start2.gro         -start2.top
        -startComplex.gro       -startComplex.top
            -startComplexContacts.top

→ The next step is to use a custom script to generate a .mdp file for the simulation. To do this, create
a new file and copy the following code (which can also be found in workflow.py from the previous
example) into the file:

NOTE If you are copying the code from workflow.py, make sure you call the createDefaultMdp() without any arguments. The default argument for this function is the one required for this example.

Code Start

 import os
 import random
 from eSBMTools import MdpFile

 path = os.getcwd() + '/'

 #we need a file that sets all the parameters of the simulation, this is the mdp file, in esbm tools
 #we use a dictionary syntax for this
 mdpDict = MdpFile.createDefaultMdp()

 #change the dictionary entries
 mdpDict['nsteps'] = 500000
 mdpDict['gen_seed'] = random.random()
 mdpDict['gen_temp'] = 138.0
 mdpDict['ref_t'] = 138.0
 MdpFile.writeMdpFile(path, 'md.mdp', mdpDict)

Code End

You can name this file custom.py (or anything else you want) and run this script using the following
command in the terminal:

            $> python custom.py

This will then create the required .mdp file for this simulation.

NOTE Do not copy the MDP file from workflow.py as it contains the graining type set to C-alpha instead of All-Atom.

→ Now that we have the files ready, we can run the simulation as normal. The steps to be followed are
exactly the same as in the previous example:

NOTE Replace startxx with the file of your choice. The startComplexContacts.top can be used with startComplex.gro

→ Run the GROMACS preprocessor with the following command:

    $> grompp -f md.mdp -c startxx.gro -p startxx.top

This will generate the corresponding mdout.mdp and the topol.tpr files.

→ Finally we run the simulation with the mdrun command as follows:

    $> mdrun -c startxx.gro

This then outputs 4 files:

            -ener.edr
            -state.cpt
            -traj.trr
            -traj.xtc

→ If all goes well, this is what your trajectory should look like (in PyMol after coloring, etc.):


And rotating it, we can see the whole structure:


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To understand the functions used in these files, view the Functions wiki.

Cheers!