ADL: protein-protein docking

Zheng Cai caizheng78 at
Wed Oct 24 15:07:00 PDT 2007

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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