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nbcrrolls / SEEKR

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.
http://amarolab.ucsd.edu/seekr/
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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:

In addition to the following nonstandard Python libraries:

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