Subject: Making A Protonated Ligand with ADT

From: tminagaw %x% purdue.edu
Date: Mon, 7 Feb 2005 13:19:50 -0500

"How to make A Protonated Ligand"

 I am using ADT(Autodock Tools) with Autodock 3.0.5
 I would like to know the way to make a "protoneted ligand"
 pdbq file.

 As you can see, benA.pdbq in Autodock 3.0.5 example(3PTB)
 has a total charge of 1.001, and I was trying to
 reproduce the same file with an original 3TB.pdb downloaded
 from Protein Data Bank.

 I extracted the ligand part (benA) from 3PTB.pdb,
 added Hydrogens and read this as a ligand molecule using ADT.
 However, ADT has assigned partial charges (Gasteiger charge) with
 a net "total" charge of zero automatically.  I need to assign a
 positive  (+1) total charge to the ligand. How do I request
 ADT to assign non-zero ligand total charges  (e.g., +1 or -1)?
 Thank you.

 Taisuke Minagawa
 Department of Physics
 Purdue University, USA