[Dock-fans] query about DOCK output

Ragothaman Yennamalli ragothaman at gmail.com
Thu Jun 9 08:24:16 PDT 2011


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
>
>  _______________________________________________
> Dock-fans mailing listDock-fans at mailman.docking.orghttp://mailman.docking.org/mailman/listinfo/dock-fans
>
> --
> ****************************************
> 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
>
> +1 515-294-8971 (Office)
> +1 515-294-8280 (Fax)
> +1 515-851-1016 (Mobile)
>
> "When
>  you can do the common things of life in an uncommon way, you will
> command the attention of the world." -George Washington Carver
>
> http://www.public.iastate.edu/~raghu/
> http://www.artistrkrishnarao.com/
>
> ***************************************
>
>
>
>
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