[Dock-fans] dock -internal energy and grid score

Mary Varughese maryvj1985 at gmail.com
Tue Feb 12 00:16:51 PST 2013


Sir,

Thank you very much. But would you please look at this output_scored.mol2
file obtained from amberscore. I use the default values in dock.in file of
the tutorial. Your opinion on the values will be helpful to me.

"rigid_scored.mol2 from the gridscore and output_scored.mol2 from
amberscore(using the  rigid_scored.mol2)"

Thanking you.

On Tue, Feb 12, 2013 at 1:07 AM, Trent E. Balius <tbalius at aol.com> wrote:

> Hi Mary,
>
>  Yes, I think that if the conformation seems reasonable to you, I would
> trust your intuition.
>
> The DOCK internal energy is not the "true" internal energy since it does
> not include dihiderals, bonds, or the attractive through space terms.
>
> You may want to re-score the conformation using a full Molecular Mechanics
> force field to get a more reasonable internal energy using for example
> Amber.  You could use AmberScore:
>
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
>
>
> I hope this helps,
> Trent
>
>  ======================================
> Trent E. Balius, PhD
> Shoichet Lab – Dept. of Pharm Chem,
> University of California, San Francisco
> 1700 4th Street
> Box 2550
> San Francisco, CA 94158
> Office: Byers Hall, Rm 509
> URL: http://docking.org/~tbalius
> ======================================
>
>
>  -----Original Message-----
> From: Mary Varughese <maryvj1985 at gmail.com>
> To: Trent E. Balius <tbalius at aol.com>
> Sent: Mon, Feb 11, 2013 11:12 am
> Subject: Re: [Dock-fans] dock -internal energy and grid score
>
>  Sir,
>
> So if the pose seems reasonable i can ignore the internal energy as high
> as 500 or above?
> What do you think about opting the conformation (on doing parallel run
> generating 5 conformations; all give the same high internal energy) having
> internal clashes.
>
> Thank you very much sir for the reply.
>
>  On Mon, Feb 11, 2013 at 10:55 PM, Trent E. Balius <tbalius at aol.com>wrote:
>
>>  Hi Mary,
>>
>> The internal energy is just the repulsive vdw term and is used to prevent
>> the molecule form clashing with itself.  This term is always positive and
>> indicates that there are internal clashes.  Visualize the molecule's dock
>> pose and see if the pose seams reasonable to you.
>>
>> See manual:
>>
>> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#InternalEnergyCalculation
>>
>>
>> To perform a "single point" calculation, where dock just will calculate
>> the energy between a pose (crystal or pergenerated) of ligand and receptor,
>> use the following parameter combination.
>>
>> orient_ligand                                                no
>> flexible_ligand                                              no
>> score_molecules                                          yes
>> minimize_ligand                                           no
>>
>> You may want to perform restrained minimization of your ligand to remove
>> clashes:
>>
>> orient_ligand                                                no
>> flexible_ligand                                              no
>> score_molecules                                          yes
>> minimize_ligand                                           yes
>>  simplex_restraint_min                                   yes
>>
>> I hope this helps,
>>
>> Trent
>>
>>  ======================================
>> Trent E. Balius, PhD
>> Shoichet Lab – Dept. of Pharm Chem,
>> University of California, San Francisco
>> 1700 4th Street
>> Box 2550
>> San Francisco, CA 94158
>> Office: Byers Hall, Rm 509
>> URL: http://docking.org/~tbalius
>> ======================================
>>
>>
>>   -----Original Message-----
>> From: Mary Varughese <maryvj1985 at gmail.com>
>> To: dock-fans <dock-fans at docking.org>
>> Sent: Sun, Feb 10, 2013 9:08 pm
>> Subject: [Dock-fans] dock -internal energy and grid score
>>
>>
>> Hi,
>>
>> I docked a ligand to a DNA. But its internal energy is very high about
>> 500.
>> Could this conformation be used.?
>> Also i want to calculate the grid score of a particular conformation.
>> So i dont want blind dock and dock in a particular region ; because with
>> a radius as small as 4.0 itself i couldnt get the particular conformation i
>> want.
>> Could i calculate dock score without allowing dock to decide the
>> conformation itself, but calculate grid score of the conformation specified
>> by me.
>> Please help me in this issue
>>
>> thanking you
>> --
>> Mary Varughese
>> Research Scholar
>> School of Pure and Applied Physics
>> Mahatma Gandhi University
>> India
>>
>> _______________________________________________
>> Dock-fans mailing listDock-fans at docking.orghttp://mailman.docking.org/mailman/listinfo/dock-fans
>>
>>
>
>
> --
> Mary Varughese
> Research Scholar
> School of Pure and Applied Physics
> Mahatma Gandhi University
> India
>



-- 
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India
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