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SEEKR: Simulation-Enabled Estimation of Kinetic Rates

Introduction
------------

WARNING: THIS SOFTWARE IS DEPRECATED AND WILL NO LONGER BE SUPPORTED. Instead,
consider using SEEKR2 which has all the features of this program along with
many improvements. SEEKR2 can be found at https://github.com/seekrcentral/seekr2.git

SEEKR (http://amarolab.ucsd.edu/seekr/) is a suite of open-source scripts and 
tools designed to enable researchers to perform multiscale computation of the 
kinetics of molecular binding, unbinding, and transport using a combination 
of molecular dynamics, Brownian dynamics, and milestoning theory.


Instructions
------------

SEEKR is designed to be run on Linux. Obtain SEEKR by cloning the Git 
repository on github.


git clone https://github.com/nbcrrolls/SEEKR.git

Or, go to the URL https://github.com/nbcrrolls/SEEKR and click the "Clone 
or download" button and save to a place in your computer.

From there, open seekr/doc/manual.txt to get started.


SEEKR is designed to run on Linux and requires the installation of the 
following software to function properly:

 - NAMD
 - BrownDye
 - LEaP (when using the Amber forcefield)
 - APBS
 - PBS (when on a supercomputer that uses PBS)
 - SLURM (when on a supercomputer that uses SLURM)

In addition to the following nonstandard Python libraries:
 - MDAnalysis
 - numpy
 - scipy

All these programs/libraries must be installed and functional before using 
SEEKR. Please consult the manuals for these programs/libraries for 
installation and usage instructions.

Files
-----

This is a description of the folders in the base seekr/ directory.
doc/ - Find detailed information about the installation, usage, tutorials, and 
  troubleshooting of SEEKR in this folder.
test/ - Most of the tests in SEEKR are integrated directly into the scripts, 
  but some tests are run externally, and are included in this directory.
namd/ - This folder contains files necessary for compiling the special build of NAMD used 
  by SEEKR.
tools/ - A number of non-essential scripts are included in this directory that 
  may be useful for calculations, preparations, and analysis.
website/ - This folder contains a full copy of the SEEKR website.


Getting Help
------------

Need help? Check out the documentation at http://amarolab.ucsd.edu/seekr/ or 
that is located in seekr/doc/manual.txt

Also, you can make comments, submit issues, and talk to real people at the 
Github site: https://github.com/nbcrrolls/SEEKR.git