ADL: protein-protein docking

Zheng Cai caizheng78 at
Wed Oct 24 16:59:14 PDT 2007

Hi Ye, Thank you so much for your quick reply.

I think the first problem will be solved following your instructions. But
for the 2nd one, I checked the output file of my first trial docking, i
found the following.

TORSDOF record detected: number of torsional degress of freedom has been set
to 600.

*** No Rotatable Bonds detected in Small Molecule. ***

>>> No torsions detected, so skipping "nonbonds", "weedbonds" and
"torNorVec" <<<

Number of atoms in ligand:  1130

Number of vibrational degrees of freedom of ligand:  3384

Number of torsional degrees of freedom = 600
Estimated loss of torsional free energy upon binding = +164.6400 kcal/mol

and this energy was used in the next steps even for clustering, and i found

DPF> ndihe 0                              # number of active torsions

./autodock4: WARNING!  The "ndihe" command is no longer supported.  The
number of torsions in the PDBQT file(s) is the number that will be used (i.e.

so do you really think this torsdof line will be ignored by AD4?  or only
the ndihe line will be ignored by AD4?
I am confused, because both "No torsions detected" and "Number of torsional
degrees of freedom = 600", could you tell me what it means? Does this
enerygy really matter?

For my case, TORSDOF 600 was defined in the last line of the
ligand.pdbqtfile. I checked the AD4 manual, and find that the only
step I skiped for
ligand preparation is the second step: Ligand->Tortion Tree->Detect Root, i
skipped this step because I found it was extremely slow for this big Ligand.
in the 3rd step, i simply chose "Make all active bonds non-rotable". Then in
the 4th step, Ligand->torsion Tree-> set number of Tortions, I typed number
0 in, and hit enter. Then I Ligand->output->Save as PDBQT..

Do you think I can skip the  "Detect Root"?  or I have to wait until the
"Detect Root" finished? Can I simply edit last line of the .pdbqt file to



Thank you so much for your time! and look forward for your reply.



On 10/24/07, Yang Ye <leafyoung at> wrote:
> 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.
> Regards,
> 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
> 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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