ADL: protein-protein docking

Zheng Cai caizheng78 at gmail.com
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
also

----------------------------------------------------------------------------------------------------------------------------------
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.
0)
----------------------------------------------------------------------------------------------------------------------------------

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

TORSDOF 0

?

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

Best,

Zheng




On 10/24/07, Yang Ye <leafyoung at yahoo.com> 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 gmail.com>
> To: autodock at scripps.edu
> 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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