Workflow Functions

This document explains the functions in eSBMTools that were used in this example.

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Abstract

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In this tutorial, we take the 2ICT protein and simulate it's behavior in an environment we set ourselves. We do this by first generting the GRO (molecular structure of the protein), the TOP (topology of the system as a whole) and a MDP file (for the parameters of the system such as temperature).

The result is a trajectory file which contains 51 states of the protein. This image shows four conformations of the simulation (1, 25, 42 and 51).

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→ Note that 4 modules from eSBMTools were imported into workflow.py:

            -GoModel.py
            -MdpFile.py
            -PdbFile.py
            -Qvalue.py

→ Now the first thing to do would be to get the PDB file, which is done with the function

    downloadPdbFile(path_to_working_directory, PDB_code)

which is used to download the PDB file of the structure whose PDB code is given to
the above function. The PDB file is downloaded from the website:

            http://www.pdb.org

This is a function of PdbFile.py

→ To create the MDP (which specifies the parameters of the system like temperature), we use

            createDefaultMdp('CA')

to first create a default MDP dictionary data type which is stored by the user. The 'CA' argument given
to this function indicates that the MDP file is to be made for the Cα model. For the All Atom model
though, the function must be called without any arguments.

As is seen in workflow.py, the parameters of the default MDP file created are changed just
like a normal Python list

        Eg.: mdpDict['nsteps'] = 500000

with the graining type provided by the user.

The MdpFile is then created by the function:

    writeMdpFile(path_to_current_directory, 'example.mdp', mdpDict)

These functions belong to MdpFile.py

→ Finally, since the graining type used in this example is Cα, a 10-12 potential is used
instead of a 6-12 potential, which is why we have to create a table.xvg file using

            writeTableCA(path)

The table.xvg has to be used whenever running simulations with Cα as the graining type.

Finally, the function

    createGoModelCA(path_to_current_directory, PDBcode,
        PDBcode + ".pdb", [], PDBcode + ".gro", PDBcode + ".top")

writes the remaining necessary files (GRO and TOP) for the simulation in the current
working directory.

This file belongs to GoModel.py

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Cheers!