[Dock-fans] Distorted bond Angles

Trent E. Balius tbalius at aol.com
Thu Jun 16 09:34:54 PDT 2011


 Hi Marco,

One way to check that dock is interpreting the torsion definition correctly is to turn on the verbose flag:  You will see data about this torsion in the verbose statistics.  See the following section from the manual.


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

Example output:

Lyr:2 Seg:0 Bond:5 : Sampling 3 dihedrals C4(C.ar) C3(C.3) C1(C.3) N1(N.3)
Lyr:2 Seg:0 57/63 retained, Pruning: 1-score 5-clustered (119 in growth tree) t=22.36s

As you can see the first line reports information about the torsion being sampled.

I am not sure but try modifying the definitions:

  name           aromatic-aromatic
  driver_id      122
  minimize       1
  
  definition     C.ar  [ 2 C.ar ]
  definition     C.ar  [ 2 C.ar ]



I would turn on the ability to minimize this torsion

The first atom type in definition is connected to the other definition via the torsion bond. 
I believe that the entries in brackets refers to the atoms connected to the first atom.

In other words, definition C.ar [2 C.ar] means that atom C.ar has two atoms connected to it of type C.ar as well as being connected to the other definition entry (I think). 

I hope this helps,  



Trent 

 

 

-----Original Message-----
From: Marco <marco at chimfarm.unipg.it>
To: dock-fans at mailman.docking.org
Sent: Thu, Jun 16, 2011 9:08 am
Subject: Re: [Dock-fans] Distorted bond Angles


Hi all, and hi Trent!

Thank you for your previous answer.
In these day I've tried to edit the flex.defn file but I get always the same
results.

I'm trying to dock a derivative of 4'Phenylcinnamic acid in my target.
If I used the rigid protocol after the predetermination of the conformers I
obtain a wonderful pose, near the experimental data I have.

But if I use the flex protocol (the classic flex.in changing only the
max_orientations to 10000) I obtain very weird poses. The orientation is
more or less good, but the two phenyl groups are planar (while I suppose
there is a little torsion since there are substituents on the aromatic
rings) and the oleifin moiety is completely out of the plane...

In the flex.defn I added the following lines aimed to sample the torsional
bond between the rings, but it doesn't work. Moreover I can't understand the
meaning of the round or squared brackets.

name           aromatic-aromatic
driver_id      122
minimize       0

definition     C.ar [ 3 C.ar ]
definition     C.ar [ 3 C.ar ]

I'm really sorry to reply my case, but I retain is a very general one, and I
guess it can be useful for other dock users.

Thank you!

----
Marco Cellanetti, 
PhD Student.
Bachelor Degree in Medicinal Chemistry and Technology of Drugs

University of Perugia
Department of Medicinal Chemistry and Drug's Technology
Via del Liceo, 1 - 06123 Perugia (Italy)
Tel ++39 075 585 5169/5114



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Per: dock-fans at mailman.docking.org <dock-fans at mailman.docking.org>
Oggetto: Dock-fans Digest, Vol 85, Issue 3
Data: 10/06/11 19:22

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> Message: 1
> Date: Fri, 10 Jun 2011 14:43:02 +0200
> From: Marco <marco at chimfarm.unipg.it>
> Subject: [Dock-fans] Distorted bond Angles
> To: dock-fans at mailman.docking.org
> Message-ID:
<a9234e3a249f8c48c79a6c9d2cab533a at iris.chimfarm.unipg.it>
> Content-Type: text/plain; charset=&quot;iso-8859-1&quot;
> 
> Hi all!
> I'm a new dock user. Following the tutorial I've performed docking studies
> on my target. I'm actually docking a small molecule with a cinnamic acid
> moiety in a flexible way. Unfortunately the olefine bond in the docking
> solution is distorted in an unnatural manner. To overcome this problem I
can
> dock in the rigid way the conformers of my small molecule, but I'd like to
> know if there is a way to set manually as rigid bond some bonds of my
> molecule.
> 
> Any advice is very appreciated. 
> Thank you.
> 
> Marco 
> 
> 
> ----
> Marco Cellanetti, 
> PhD Student.
> Bachelor Degree in Medicinal Chemistry and Technology of Drugs
> 
> University of Perugia
> Department of Medicinal Chemistry and Drug's Technology
> Via del Liceo, 1 - 06123 Perugia (Italy)
> Tel ++39 075 585 5169/5114
> 
> 
> 
> 
> ________________________________________________________________
> Message sent using Telaen Webmail 1.2.0
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 10 Jun 2011 10:03:43 -0400
> From: &quot;Trent E. Balius&quot; <tbalius at aol.com>
> Subject: Re: [Dock-fans] Distorted bond Angles
> To: marco at chimfarm.unipg.it, dock-fans at mailman.docking.org
> Message-ID: <8CDF58E57EE6BE1-16E0-981FA at webmail-m137.sysops.aol.com>
> Content-Type: text/plain; charset=&quot;us-ascii&quot;
> 
> 
>  Hi Marco,
>     
> One approach to sample this distorted torsion is to modify the flex.defn
and the flex_drive.tbl files.
>     
> See the following:
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#flexdefn
>   http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#flex_drivetbl
> In addition consult the following:
> http://mailman.docking.org/pipermail/dock-fans/2010-May/002360.html
> 
> Excerpt from flex.defn:
> name sp3-sp3 
> drive_id 3 
> minimize 1 
> definition .3 [ 3 H ] [ 3 O.co2 ] 
> definition .3 [ 3 H ] [ 3 O.co2 ] 
>     
> Here you can see the the flexible definition file specifies a torsion
angle and gives the drive type (drive_id). 
>     
>   Excerpt from flex_drive.tbl
> drive_id 3 
> positions 3 
> torsions -60 60 180 
> 
>  
> Here you can see that the flexible drive table specifies the angle to be
sampled for the drive type.
> 
> You should modify the flex.defn to have an entry for the olefine bond and
use of create an appropriate entry in the flex_drive.tbl file.
>   
> You may want to also verify that your small molecule mol2 file has the
correct hybridization and protonation.  
> 
> 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: Marco <marco at chimfarm.unipg.it>
> To: dock-fans at mailman.docking.org
> Sent: Fri, Jun 10, 2011 8:43 am
> Subject: [Dock-fans] Distorted bond Angles
> 
> 
> Hi all!
> I'm a new dock user. Following the tutorial I've performed docking studies
> on my target. I'm actually docking a small molecule with a cinnamic acid
> moiety in a flexible way. Unfortunately the olefine bond in the docking
> solution is distorted in an unnatural manner. To overcome this problem I
can
> dock in the rigid way the conformers of my small molecule, but I'd like to
> know if there is a way to set manually as rigid bond some bonds of my
> molecule.
> 
> Any advice is very appreciated. 
> Thank you.
> 
> Marco 
> 
> 
> ----
> Marco Cellanetti, 
> PhD Student.
> Bachelor Degree in Medicinal Chemistry and Technology of Drugs
> 
> University of Perugia
> Department of Medicinal Chemistry and Drug's Technology
> Via del Liceo, 1 - 06123 Perugia (Italy)
> Tel ++39 075 585 5169/5114
> 
> 
> 
> 
> ________________________________________________________________
> Message sent using Telaen Webmail 1.2.0
> 
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