ADL: protein-protein docking

Zheng Cai caizheng78 at gmail.com
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
coefficient

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!

David.
-- 
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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