KPrep

KPrep Introduction

Short for Knotts group Preparation scripts, KPrep is a series of python packages that streamlines the process of creating input scripts for various simulators. Additional contributions have added many features for protein manipulation. These features are described in subsequent pages. Included on this page is general set-up and uses. If you are a part of this group feel free to make these scripts better.

You can get a copy of these scripts from the group folder on the super computer.

To use KPrep you need to implement them using standard python package procedure. Put the files in the pathway indicated by PYTHONPATH. If put here you can access it anywhere on your computer. You can also put these files in the directory where you are running python script. If put in both described location, the directory location trumps the PYTHONPATH location. Use this method for editing KPrep to make sure you have a stable version. Do not overwrite the version in the group folder on the supercomputer unless you know you have a stable version.

KPrepInfo

The general method for preparation is to use the pseudo object-based coding in python. Within KPrepInfo we define an "interacting site" object. Because we assume a CHARMM-like atom from a pdb file, these objects are called "atoms," but KPrep is also coded to create Go-model input files where an atom object is a Go-model amino acid interacting site. This file is necessary for the read and write scripts within KPrep. For additional information about the information stored in atom objects, please read the comments in the KPrepInfo.py file.

KPrepRead

The scripts in this file are designed to read files directly taken from the internet and convert them into "atom" sites.

KPrepWrite

These scripts take "atom" sites and writes file that are simulation-ready or near-simulation-ready.