Simulation Enables Estimation of Kinetic Rates (SEEKR): a Multiscale Simulation Approach for Calculating Binding Kinetics

In this tutorial, you will learn the basics of setting up a SEEKR simulation to calculate the binding kinetics of a model host-guest system, beta-cyclodextrin with aspirin.

You will:

1. Prepare the SEEKR input file
2. Run SEEKR to prepare the milestone systems
3. Visualize simulation trajectories
4. Construct a milestoning model and calculate rates
5. Perform convergence analysis

Obtaining the latest version of SEEKR

The latest version of SEEKR can be cloned or downloaded through the NBCR github: https://github.com/nbcrrolls/SEEKR

Additional information about SEEKR can be found in SEEKR/doc/manual.txt.

SEEKR Requirements

To run a complete SEEKR calculation, you will need the following installed:

• VMD for visualization http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
• NAMD molecular dynamics package http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD
• BrownDye for BD simulations https://browndye.ucsd.edu/
• LEaP when using the AMBER forcefield http://ambermd.org/GetAmber.php
• APBS for electrostatics calculations http://apbs-pdb2pqr.readthedocs.io/en/latest/downloads.html
• Python version 2 (2.7 or later) with the following packages (I recommend using Anaconda):
  • numpy
  • scipy
  • MDAnalysis
  • matplotlib
  • dill

SEEKR Tutorials

This repository contains two tutorails:

The abbreviated tutorial abbrev_tutorial.md focuses entirely on visualizing and analyzing the results of a SEEKR calculation and does not require the installation of many of the packages used for system preparation.

The complete tutorial complete_tutorial.md covers system preparation, generation of simulation files, running simulaitons, and analysis. This requires the installation of all packages (specifically LEaP and APBS for system prep).