[Dock-fans] Regarding Dock6

William Joseph Allen william.joseph.allen at gmail.com
Mon Jun 1 06:22:10 PDT 2015


Hi Gaurav,

May I ask, why do you need exactly 30 poses? If you set
num_scored_conformers to 5000 and obtain 70 poses, it would be relatively
easy to skim off the first 30 poses in the output file.

Now that I see the small size of your ligand, another thing to try occurs
to me. You could increase max_orientations to a very large number, e.g.
10000. I am not sure exactly how this may affect the number of final poses,
but if you pair that with num_scored_conformers = 30, you may get your
desired result.

Joe




On Mon, Jun 1, 2015 at 1:02 AM, <gauravkishor at imtech.res.in> wrote:

>  Hello Sir,
>
> As per your guidance i used "rigid.in" provided by you. Still i am unable
> to solve my problem. I need 30 poses of a ligand so i run dock6 by editing
> "num_scored_conformers 30", but i am not getting desirable results.When i
> am changing this value, i am getting as following:
>
>                                             value             no. of mol2
> in rigid_scored.mol2
>
> num_scored_conformers           10                              5
>
> num_scored_conformers           20                              7
>
> num_scored_conformers           30                              9
>
> num_scored_conformers           40                             10
>
> num_scored_conformers        5000                             70
>
> I am herewith attaching my input files for your convenience, pleasae help
> me for that i'll be grate full to you.
>
>
>
> Gaurav Kishor
>
> Project Fellow
>
> CSIR-IMTECH
>
> Chandigarh,India
>
>  18:43, William Joseph Allen wrote:
>
> 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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