Menu
▾
▴
Home
Welcome to the eSBMTools Wiki
eSBMTools are Python tools used for enhanced native structure-based modeling of proteins and nucleic acids, both at the Cα and all-atom level. The tools interface with GROMACS and support its standard output formats.
eSBMTools is a powerful package that makes the job of running simulations much easier. They can generate the necessary files for running the simulations with GROMACS, compile data from several simulations, produce free energy graphs, make histograms and a lot more. Above all, they are designed to be simple to use and understand for the user.
The tools are also well documented so that you can write your own python scripts for more complex problems and for a better control over the simulation. To help you get a feel of what eSBMTools can do and their capabilities, a few examples have been compiled and are available in the package itself.
This wiki is designed to help you run the examples and understand the functions used within that are provided with eSBMTools. There are a total of five examples and below are the links to their tutorials. After reading through these pages and understanding the working of these tools, you should be able to write your own custom scripts using eSBMTools.
There are 2 texts for each of the examples:
-
Tutorial - which contains the steps for running the simulations
-
Functions - explaining the functions used in the python script of the example.
Workflow
Tutorial
Functions
The simulation followed in this example is of the protein 2ICT using the Cα model. It is recommended that you use this as your first example as this will give you a basic idea of how the workflow of running a simulation is, what the different steps are and what happens during each step.
Complex Formation
Tutorial
Functions
A protein complex, which as the name suggests, is formed from multiple proteins. eSBMTools can also be used to form a complex as illustrated in this example where the proteins 1IXM and 1PEY are bound together to form 1F51.
Contact Map Visualization
Tutorial
Functions
The contact map of a protein is a particularly useful representation in that it does not change with the rotation or translation of a protein. This example uses eSBMTools to calculate the Q values of a protein and draw it's contact map using 3 methods: with the protein's topology, with MJ weighting and through it's trajectory.
Free WHAM
Tutorial
Functions
It is common practice to view the information of a simulation in the form of free energy graphs. This is something eSBMTools can used for, as shown in this example, where the results of a simulation from a range of temperatures are taken and plotted in a free energy graph.
Q Histogram
Tutorial
Functions
eSBMTools can also be used to show histograms of graphs from simulations with it's built in tools as shown in this short example.
Sincerely yours,
Project Admins:
