/CYS-Bonds

Provide a pdb file, and this will write tleap bond commands for you.

Primary LanguageC++

CYS-bonds

Uses GEMS/GMML to figure out which CYS residues should be bonded to each other based on distance, then writes tleap bonds commands.

Prerequisites

You'll need GEMS and GMML. See here for installation instructions: http://glycam.org/docs/gems/download-and-install/.

2017-06-28 you'll need the gmml-dev branch:

git clone -b gmml-dev https://github.com/GLYCAM-Web/gmml.git gmml

Installation of CYS-bonds

export GEMSHOME= # eg: export GEMSHOME=/home/oliver/Programs/gems

qmake

make

Usage

You must provide a protein 3D structure

./CYS-bonds protein.pdb

Warning

Crashes out if your input file does not exist or you do not provide one, but if you've read this far that shouldn't be happening..