[Dock-fans] Regarding Dock6

William Joseph Allen william.joseph.allen at gmail.com
Thu May 28 06:13:14 PDT 2015


Hi Gaurav,

More information about the ligand file outputs can be found in this section
of the manual:

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileOutput

More to your question, the files that you are seeing when you set
"write_conformations = yes" are all of the conformers generated, beginning
from each anchor, that pass the final level of optimization. There will be
a lot of redundancy among these files and I don't think it is exactly what
you are looking for.

One thing I will also note is that in rigid docking, the molecule is
treated as inflexible. This means the 3D internal geometry of the molecule
will not change from your input, only rigid-body rotational and
translational degrees of freedom will be sampled. If this is your
objective, then you are heading down the right path. However, if you wish
to sample the internal degrees of freedom of your input ligand, then you
will need to perform what is called flexible docking.

Now I have not seen your input file, but there is a parameter near the end
called "num_scored_conformers". If this is set to "1", only the singular,
top-scoring compound will be written, which sounds like what you are
observing. If you set it to a very large number, e.g. "5000", then many
more final poses will be written. Please try to re-run your docking
calculations with the following input files to see if you observe better
results.

Flexible docking: http://george.ams.sunysb.edu/SB2010/FLX.in
Rigid docking: http://george.ams.sunysb.edu/SB2010/RGD.in

Note that some of the input values will need to change according to your
environment / file locations / file names. These are the generally
recommended input parameters used by our group. Let me know if you have any
other questions.

Joe Allen



On Wed, May 27, 2015 at 11:11 PM, <gauravkishor at imtech.res.in> wrote:

>  Dear Sir,
>
> This is Gaurav kishor,project fellow at CSIR-IMTECH,INDIA. In order to
> solve my problem, i am using dock6 as a docking tool. I want to
> generate 30 poses of a ligand. But unfortunately i am getting only one
> output file called "rigid_ranked.mol2". By making some changes in
> "rigid.in", i got one more file called rigid_conformers.mol2. I am
> unable to understand this file what exactly it is and how to analyze.
> I have gone through the Dock6 manual but i could resolve this. I need
> your guidance.
>
> example of rigid_conformers.mol2 that i am getting:
>
> lig.pdb_1
>
> lig.pdb_1
>
> lig.pdb_2
>
> lig.pdb_1
>
> lig.pdb_2
>
> lig.pdb_3
>
> lig.pdb_1
>
> lig.pdb_2
>
> lig.pdb_3
>
> lig.pdb_4.........
>
> Thakyou
>
>
>
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>
>
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