Subject: charged ligand for autodock

From: Susan Heffron <[email-masked]>
Date: Tue, 28 May 2002 13:28:45 -0700

Dear Autodock users,

What is the best way to assign charges to an ionized ligand for docking
with Autodock?  I have been using AutoDockTools to add Gasteiger charges
to my ligands, and then editing the pdbq file to remove a hydrogen and
add a -1 charge to the nitrogen that is ionized.  But I'm sure that
isn't an accurate way to do it.  If I remove the hydrogen before feeding
the coordinates to ADT, the charges are different, but the overall
charge is 0.0 (neutral), which isn't what I want.  Is there any way to
tell ADT that a ligand should be charged?  If not, how should I
calculate, or approximate, the partial charges on my ionized ligand?  

                              Susan

                                                     O
                                                     "
P.S.  The group on the ligand that is ionized is    -S-NH2
                                                     "
                                                     O

-- 
------------------------------------------------------------------
        Susan Heffron
Dept. of Physiology and Biophysics                               
University of California, Irvine                
 Irvine, CA  92697-4560   U.S.A.                         
    phone:  (949) 824-4625
    FAX:    (949) 824-8540
------------------------------------------------------------------