ADL: Feature Request

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

ADL: Feature Request

Matthew Lardy
Hi,

I hope this isn't too big of a request.  Could someone break out the terms
of the scoring function and put that in the output of Vina?  Let me know if
I can help.

Thanks!
Matt
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: Feature Request

Ruth Huey
Here's a possible two_step work-around:
FIRST  use vina_split (which is included in the bin directory of the vina download) to split the vina result into separate models:
~$PATH_TO_VINA/bin/vina_split --input 1dif_random_out.pdbqt

9 separate files are created for this particular vina result:
1dif_random_out_ligand_1.pdbqt  1dif_random_out_ligand_5.pdbqt  1dif_random_out_ligand_9.pdbqt
1dif_random_out_ligand_2.pdbqt  1dif_random_out_ligand_6.pdbqt  
1dif_random_out_ligand_3.pdbqt  1dif_random_out_ligand_7.pdbqt
1dif_random_out_ligand_4.pdbqt  1dif_random_out_ligand_8.pdbqt

NEXT use vina with the option 'score_only' to print the terms of the scoring function for each of these:

~$PATH_TO_VINA/bin/vina --ligand 1dif_random_out_ligand_1.pdbqt --score_only --receptor ../hsg1.pdbqt

#################################################################
# If you used AutoDock Vina in your work, please cite:          #
#                                                               #
# O. Trott, A. J. Olson,                                        #
# AutoDock Vina: improving the speed and accuracy of docking    #
# with a new scoring function, efficient optimization and       #
# multithreading, Journal of Computational Chemistry 31 (2010)  #
# 455-461                                                       #
#                                                               #
# DOI 10.1002/jcc.21334                                         #
#                                                               #
# Please see http://vina.scripps.edu for more information.      #
#################################################################

Detected 2 CPUs
Reading input ... done.
Setting up the scoring function ... done.
Affinity: -10.31896 (kcal/mol)
Intermolecular contributions to the terms, before weighting:
    gauss 1     : 163.65647
    gauss 2     : 2902.55105
    repulsion   : 4.22156
    hydrophobic : 95.41157
    Hydrogen    : 3.05689

________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Matthew Lardy [[hidden email]]
Sent: Wednesday, July 23, 2014 11:53 AM
To: [hidden email]
Subject: ADL: Feature Request

Hi,

I hope this isn't too big of a request.  Could someone break out the terms
of the scoring function and put that in the output of Vina?  Let me know if
I can help.

Thanks!
Matt
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: Feature Request

Matthew Lardy
Hi Ruth,

Thanks, I just wasn't aware that rescoring molecules would break out the
values for the hydrogen-bonding, hydrophobic, etc., interactions.  It would
be nice, per docking solution, for these to be placed in the output.  I
started to modify the source to do exactly that, but I wouldn't want any
personal modifications to be out of step with the development tree.

Thanks for answering so quickly!
Matt


On Wed, Jul 23, 2014 at 3:12 PM, Ruth Huey <[hidden email]> wrote:

> Here's a possible two_step work-around:
> FIRST  use vina_split (which is included in the bin directory of the vina
> download) to split the vina result into separate models:
> ~$PATH_TO_VINA/bin/vina_split --input 1dif_random_out.pdbqt
>
> 9 separate files are created for this particular vina result:
> 1dif_random_out_ligand_1.pdbqt  1dif_random_out_ligand_5.pdbqt
>  1dif_random_out_ligand_9.pdbqt
> 1dif_random_out_ligand_2.pdbqt  1dif_random_out_ligand_6.pdbqt
> 1dif_random_out_ligand_3.pdbqt  1dif_random_out_ligand_7.pdbqt
> 1dif_random_out_ligand_4.pdbqt  1dif_random_out_ligand_8.pdbqt
>
> NEXT use vina with the option 'score_only' to print the terms of the
> scoring function for each of these:
>
> ~$PATH_TO_VINA/bin/vina --ligand 1dif_random_out_ligand_1.pdbqt
> --score_only --receptor ../hsg1.pdbqt
>
> #################################################################
> # If you used AutoDock Vina in your work, please cite:          #
> #                                                               #
> # O. Trott, A. J. Olson,                                        #
> # AutoDock Vina: improving the speed and accuracy of docking    #
> # with a new scoring function, efficient optimization and       #
> # multithreading, Journal of Computational Chemistry 31 (2010)  #
> # 455-461                                                       #
> #                                                               #
> # DOI 10.1002/jcc.21334                                         #
> #                                                               #
> # Please see http://vina.scripps.edu for more information.      #
> #################################################################
>
> Detected 2 CPUs
> Reading input ... done.
> Setting up the scoring function ... done.
> Affinity: -10.31896 (kcal/mol)
> Intermolecular contributions to the terms, before weighting:
>     gauss 1     : 163.65647
>     gauss 2     : 2902.55105
>     repulsion   : 4.22156
>     hydrophobic : 95.41157
>     Hydrogen    : 3.05689
>
> ________________________________________
> From: [hidden email] [[hidden email]] On
> Behalf Of Matthew Lardy [[hidden email]]
> Sent: Wednesday, July 23, 2014 11:53 AM
> To: [hidden email]
> Subject: ADL: Feature Request
>
> Hi,
>
> I hope this isn't too big of a request.  Could someone break out the terms
> of the scoring function and put that in the output of Vina?  Let me know if
> I can help.
>
> Thanks!
> Matt
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---