[Dock-fans] query about DOCK output

Trent E. Balius tbalius at aol.com
Thu Jun 9 09:47:08 PDT 2011


 Hi Ragothaman,

It seems that all your anchors orients are immediately pruned away.

This error is most likely do to the fact the your anchors have a vary unfavorable (positive) internal energy.

I would increase the parameter for score cutoff for pruning:

pruning_conformer_score_cutoff                               1000.0

This parameter is used to eliminate poses with Dock energies that exceed the cutoff or with internal energy that exceeds the cutoff.  Although, by making the cutoff this high you are letting very unfavorable poses through.  

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: Ragothaman Yennamalli <ragothaman at gmail.com>
To: Trent E. Balius <tbalius at aol.com>; John Irwin <jir322 at gmail.com>; dock-fans at mailman.docking.org
Sent: Thu, Jun 9, 2011 11:24 am
Subject: Re: [Dock-fans] query about DOCK output


Hi,
This is a followup of the previous email, where I used DOCK 6.4 and used the internal energy parameters. Few molecules that were docked successfully earlier in dock 6.2, did not dock in this setting. Here is the verbose output for the molecule. I have used max_orientations as 1000. Can someone please tell me how to resolve this error?
Thanks in advance,
Ragothaman
-----------------------------------
VERBOSE MOLECULE STATS

  Number of heavy atoms = 40
  Number of rotatable bonds = 23
  Formal Charge = 4.00
  Molecular Weight = 585.61
  Heavy Atoms = 40
Orienting 11 anchor heavy atom centers
-----------------------------------
VERBOSE GROWTH STATS : ANCHOR #1

0/100 anchor orients retained (max 100) t=5.16s
Lyr 1-5 Segs|Lyr 2-2 Segs|Lyr 3-4 Segs|Lyr 4-2 Segs|Lyr 5-5 Segs|Lyr 6-3 Segs|Lyr 7-1 Segs|Lyr 8-1 Segs|
Lyr:1 Seg:0 0/0 retained, Pruning:  t=5.2s
Lyr:1 Seg:1 0/0 retained, Pruning:  t=5.2s
Lyr:1 Seg:2 0/0 retained, Pruning:  t=5.2s
Lyr:1 Seg:3 0/0 retained, Pruning:  t=5.2s
Lyr:1 Seg:4 0/0 retained, Pruning:  t=5.2s
Lyr:2 Seg:0 0/0 retained, Pruning:  t=5.2s
Lyr:2 Seg:1 0/0 retained, Pruning:  t=5.2s
Lyr:3 Seg:0 0/0 retained, Pruning:  t=5.2s
Lyr:3 Seg:1 0/0 retained, Pruning:  t=5.2s
Lyr:3 Seg:2 0/0 retained, Pruning:  t=5.2s
Lyr:3 Seg:3 0/0 retained, Pruning:  t=5.2s
Lyr:4 Seg:0 0/0 retained, Pruning:  t=5.2s
Lyr:4 Seg:1 0/0 retained, Pruning:  t=5.2s
Lyr:5 Seg:0 0/0 retained, Pruning:  t=5.2s
Lyr:5 Seg:1 0/0 retained, Pruning:  t=5.2s
Lyr:5 Seg:2 0/0 retained, Pruning:  t=5.2s
Lyr:5 Seg:3 0/0 retained, Pruning:  t=5.2s
Lyr:5 Seg:4 0/0 retained, Pruning:  t=5.2s
Lyr:6 Seg:0 0/0 retained, Pruning:  t=5.2s
Lyr:6 Seg:1 0/0 retained, Pruning:  t=5.2s
Lyr:6 Seg:2 0/0 retained, Pruning:  t=5.2s
Lyr:7 Seg:0 0/0 retained, Pruning:  t=5.2s
Lyr:8 Seg:0 0/0 retained, Pruning:  t=5.2s

-----------------------------------
Molecule: molecule1.sdf

 Elapsed time:  13 seconds

 ERROR:  Could not complete growth.
         Confirm that the grid box is large enough to contain the ligand,
         and try increasing max_orientations.




On Wed, May 25, 2011 at 4:26 PM, Trent E. Balius <tbalius at aol.com> wrote:

 Hi  Ragothaman,
    
DOCK 6.4 now has the ability to perform growth with an Internal Energy function (only the repulsive VDW term) which will prevent ligand internal clashes.  
    
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#InternalEnergyCalculation
 
use_internal_energy                       yes
internal_energy_rep_exp                 12

There is also the "use_clash_overlap" parameter discussed in the section on flexible ligand:

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

"use_clash_overlap" is a "flag to check for overlapping atomic volumes during anchor and grow." 

You may wish to use this parameter in conjunction or instead of the internal energy. However, if you do not use the internal energy parameter, sometimes you may get "could not complete growth" errors due to the fact that all poses were pruned.  the internal energy function is used during growth and minimization which allows the minimizer to rescue poses that would other wise be pruned.

I hope that 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: Ragothaman Yennamalli <ragothaman at gmail.com>
To: dock-fans at mailman.docking.org
Sent: Wed, May 25, 2011 4:17 pm
Subject: [Dock-fans] query about DOCK output


Hi,
I am able to successfully run DOCK with my small molecules and the results come out fine (No errors). However, when I vizualize the docked conformation I see that some of the molecules have unusual conformations, that are impossible to happen. For eg: If the molecule has three rings, the docked conformation looks like a folded shape, where the first and third ring are touching each other. I am sure there must be penalties built in to check these kind of structures. How to prevent dock from doing this?
I am open to all suggestions.

Thanks and Regards,
Ragothaman


 


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Ragothaman M Yennamalli, Ph.D.

Postdoctoral Research Associate

1012 Crop Genome Informatics Laboratory



Department of Genetics, Development and Cell Biology

Iowa State University

Ames, Iowa 50011-3260 USA



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