ADL: How to make A Protonated Ligand
tminagaw at purdue.edu
Mon Feb 7 09:15:56 PST 2005
"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"
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)?
Department of Physics
Purdue University, USA
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