Subject: help regarding Autodock

From: "Ankit Soni" <ankit=at=iitk.ac.in>
Date: Wed, 16 Jun 2004 15:08:16 +0530

Hi  CClers:

         I have just started using Autodock3 and don`t have an extensive
background of docking theory.could someone please clarify some of
my doubts.
1) what is the criteria for docking is it min energy or is it min RMSD??
2) If we want to calculate the RMSD from a reference file what should be
the format of the input reference file and can ADT(Autodock tool kit) create it..or can we get it from PDB.
3) also can any one suggest some reference for the Directional H-bond
implementation  in autogrid based on Goodford or explain the
theory behind the process.

If anyone can help me I would be highly obliged.

Thank You

Sincerely,

Ankit

Ankit Soni 
Junior Undergraduate
Department of Computer Science and Engineering,
Indian Institute of Technology Kanpur