Glide is a well-known ligand docking program developed by SCHRODINGER (http://www.schrodinger.com/productpage/14/5/). This tutorial describes how to dock a library of small ligands on a RNA receptor (also applicable to protein receptors). We will use both the ugly command-line approach and the graphical user interface maestro program throughout the docking procedure and we will see that there are advantages for both. This tutorial is for a docking beginner and you can refer to the online user manuals if you are seeking more details or flexibility for any step.
The docking procedure with glide has some different steps:
A- Receptor preparation
B- Grid Generation
C- Ligands preparation
D- Docking and Analysis of docking poses
The first step to use glide as well as other related SCHRODINGER programs in unix environment is to have the SCHRIDONGER address in your path. So if you are using CHPC Utah, you can add the following lines to your ~/.tcshrc file.
setenv SCHRODINGER //uufs/chpc.utah.edu/sys/pkg/Schrodinger/2012
setenv SCHROD_LICENSE_FILE @flexvm.inscc.utah.edu
set path = ($SCHRODINGER $path)
Glide is optimized for protein receptors, but it can also prepare nucleic acids. We will prepare the crystal structure of domain 2 of HCV IRES RNA with the PDB code 3TZR. To start preparing, run maestro program from your command line. The following window will open in few seconds: