ADL: Is there a minimum size for the grid box??

Wim Nerinckx wimnerinckx at lavabit.com
Fri Oct 30 07:11:19 PDT 2009


Maybe your gridbox is not properly centered versus the recognition site.
Wim, Belgium

On 30 Oct 2009, at 14:43, Jerome Baffreau wrote:

>
> Hi all,
>
> recently I prepared several Autodock calculations (4.2) with a  
> series of
> ligands and 2 different proteins. After a while I saw that final  
> binding
> energies were in the range of +100,000 kcal/mol for all of them!!
>
> Then I changed the grid box dimensions from 36;38;40 to 36;60;40  
> and it
> worked fine, I got binding energies around -20 kcal/mol... And you  
> know
> what? If I use 36;58;40 energies are back in the +100,000 kcal/mol  
> range...
> wierd, or do I do something wrong?
>
> This was with the first protein... but I experienced the same issue  
> with the
> other one, instead of 40;40;42 I had to use 46;56;42 as minimum box  
> size in
> order to get correct binding energies.
>
> Does anybody already experienced such issue, or does anybody know  
> where it
> could come from?
>
> Thanks for your help.
>
> -----
> Jerome
>
> ¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤
> Jerome Baffreau, PhD
> Universite de Montreal
> Montreal, QC - CANADA
>
> -- 
> View this message in context: http://n2.nabble.com/Is-there-a- 
> minimum-size-for-the-grid-box-tp3918971p3918971.html
> Sent from the AutoDock mailing list archive at Nabble.com.
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/ 
> mailing_list ---





More information about the autodock mailing list