Subject: Covalent map in Autodock and Autodocktools

From: olivier walker <[email-masked]>
Date: Fri, 01 Nov 2002 16:26:27 -0800

Hi,

To explore the conformation of a dual domain protein, I use Autdock and 
Autodocktools, making one domain the ligand (I'm just interested in 
rotating 20 bounds for the 6 residues of the linker) and the other one the 
macromolecule. I've several questions regarding these two programs:

1) When I create pdbq files from mol2 files (from InsightII), I obtrain 
completely different files. The file created by Autodock utility program 
mol2topdbq is fine, but the one created by Autodocktools adds a bunch of 
''CONNECT'' word that autodock3 couldn't understand. What did I wrong?

Thus, I'm using the command line to create input files to use with 
autodock3. The most important issue is that I need the extremity of my 
linker to be stick with the macromolecule.

2) How to create a covalent map with Autodock or Autodocktools?
         a) With Autodocktools, I tried to select an atom on the 
macromolecule and then create a covalent map but when I click on the box 
''use selection'', I always receive the same message "incorrect ligand file 
format-unable to write with Z atom".

         b) How to create such a covalent map with Autogrid and how to 
specify the 2 atoms I want to be linked? I read the manual or the tutorial 
for these two programs, but this section is not well documented.

I will appreciate any help.

Olivier

**************************************************
Olivier WALKER
Department of Chemistry & Biochemistry
University of Maryland
College Park, MD 20742
USA
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Fax : 301-314-0386
Phone : 301-405-8710
E-mail : [email-masked]
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