ADL: protein-protein docking

Yang Ye leafyoung at
Wed Oct 24 15:25:57 PDT 2007

1. You can work around this by having an understanding of the pdbqt file and manual editing. When atoms are placed in one block with ROOT/ENDROOT or BRANCH/ENDBRANCH, they become relative fixed to each other. First, generate two pdbqt files for each part of the ligand. Identify their "bonding" parts and paste two files together.

2. This line will be ignored by AD4. I am curious why there are 600 TORS for the ligand. Please check your ligand and procedure of preparation.
Yang Ye

----- Original Message ----
From: Zheng Cai <caizheng78 at>
To: autodock at
Sent: Thursday, October 25, 2007 6:07:00 AM
Subject: ADL: protein-protein docking

Hi autodockers!

I am trying to use autodock4 to do a antibody-antigen docking. The antigen
protein( 2 chains) was simply considered  as Macromolecular. And the
antibody Fab (also 2 chains) was considered as ligand. I met several
troubles as following when I run the program. I wonder if any of you had the
same problem before and could kindly help me out?

1. two chain ligand.  it seems autodock4 can only deal with 1-chain ligand,
if i load the two-chain coordinate in, it will simply output the first chain
it read, while the second chain was lost. (fortunately, there is no trouble
for a two-chain macromolecule)

2. for the torsdof parameter in the .dpf file, I saw the value below

torsdof  600 0.274000          # torsional degrees of freedom and

for my understanding, this parameter should be set as 0 in the
protein-protein rigid docking case, am i correct? if it is, can I manually
edit this line in the .dpf file to:

torsdof  0 0.274000          # torsional degrees of freedom and coefficient

Any input will be greatly appreciated!

All my best regards!

Zheng Cai, Ph.D.
Department of Pathology and Laboratory Medicine
University of Pennsylvania School of Medicine
252 John Morgan Building
36th Street and Hamilton Walk
Philadelphia, PA 19104
(lab-tel) 215-898-2870
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