[Dock-fans] "Fixed Anchor Docking"

Trent E. Balius tbalius at aol.com
Mon May 17 12:46:42 PDT 2010



 Hi Dariusz,

You will want to look at the flex.defn file:

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

copy the  "flex.defn" file (from dock distribution in dock6/parameters/flex.defn) and manually modify to include definition of only the bonds you would like.

See 
    
http://ringo.ams.sunysb.edu/index.php/Optimize_Polar_Hydrogens 
  
 
for an example that will only move polar hydrogens.


Custom atom types may need to be defined and used. 

Good luck,


Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Dariusz Ekonomiuk <ekodarek at icm.edu.pl>
To: Sudipto Mukherjee <sudmukh at yahoo.com>; Trent E. Balius <tbalius at aol.com>
Sent: Mon, May 17, 2010 10:49 am
Subject: "Fixed Anchor Docking"


Dear Trent and Sudipto,

I have one question related to the "Fixed Anchor Docking" procedure you
use in the group.
Do you know how to include in anchor definition more atoms (or different
atoms) than those identified automatically by DOCK ?

I tried to do that with "Manual Specification of Non-rotatable Bonds"
by defining @<TRIPOS>SET, but it seems that the new version of DOCK still
doesn't take this information into account.

looking forward to your reply.

best regards,
       Dariusz


> Hi,
>
> We actually call it "Fixed Anchor Docking", as in the ligand anchor
> position is fixed to the 'correct' location, and the torsions are grown
> out.
>
> Regards
> Trent E. Balius
> Sudipto Mukherjee
>
>
>
> ________________________________
> From: Dariusz Ekonomiuk <ekodarek at icm.edu.pl>
> To: Trent E. Balius <tbalius at aol.com>
> Cc: dock-fans at mailman.docking.org
> Sent: Tue, April 27, 2010 1:26:08 PM
> Subject: Re: [Dock-fans] anchor orientation
>
>
> Thank you Trent
> "Fix Anchor Docking" is what I was looking for.
>
> best,
>   Dariusz
>
>>
>>
>>  Hi Dariusz,
>>
>> You can turn off ligand orientation by the following:
>>
>>   orient_ligand    no
>>   flexible_ligand  yes
>>
>> This will grow out your ligands starting from the anchor in your
>> beginning
>> orientation.
>> In the Rizzo group, we call this procedure Fix Anchor Docking.
>>
>>
>> Note that the anchor will still move because of the simplex minimizer.
>>
>> I hope this helps,
>>
>>
>>
>> Trent E. Balius
>> Graduate Student, Rizzo Group,
>> Department of Applied Mathematics and Statistics,
>> Stony Brook University.
>> Office: Math Tower 3-129, Phone: (631) 632-8519
>> URL: http://www.ams.sunysb.edu/~tbalius/
>>
>>
>>
>>
>>
>> -----Original Message-----
>> From: Dariusz Ekonomiuk <ekodarek at icm.edu.pl>
>> To: dock-fans at mailman.docking.org
>> Sent: Tue, Apr 27, 2010 5:10 am
>> Subject: [Dock-fans] anchor orientation
>>
>>
>> Dear all,
>>
>> I have a question related to anchor and grow algorithm as implemented in
>> DOCK 6.3.
>> Would it be possible to use user defined orientation of the anchor ?
>> In other words, I would like to start with predefined coordinates of the
>> anchor and then use DOCK
>> for growing the layers.
>> I assume it would require modifications in the source code,
>> any hints ?
>>
>> best,
>> Dariusz Ekonomiuk
>>
>> _______________________________________________
>> Dock-fans mailing list
>> Dock-fans at mailman.docking.org
>> http://mailman.docking.org/mailman/listinfo/dock-fans
>>
>>
>>
>
>
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>
>
>
>


 
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