ADL: Is there a minimum size for the grid box??
wimnerinckx at lavabit.com
Fri Oct 30 07:11:19 PDT 2009
Maybe your gridbox is not properly centered versus the recognition site.
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
> 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
> what? If I use 36;58;40 energies are back in the +100,000 kcal/mol
> 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 Baffreau, PhD
> Universite de Montreal
> Montreal, QC - CANADA
> View this message in context: http://n2.nabble.com/Is-there-a-
> Sent from the AutoDock mailing list archive at Nabble.com.
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