ADL: Help please!!!

Boris Gorelik bgbg at
Mon May 22 23:58:41 PDT 2006

The "Introductory tutorial for Autodock 
3.0" ( )
says the following (page 26):

D. Run Autogrid
autogrid3 –p dna.gpf –l dna.glg &
As this calculation runs in background, you may receive a few warnings. Just 
hit enter and ignore these. ..........
These warnings are exactly the ones you are talking about. 
So I assume it's OK to ignore them. I get reasonable results with most of my 
docking  calculations, despite the fact that the "division by zero" warning 
appears in each of them.

On Tuesday, 23 בMay 2006 00:50, Joanne Hanna wrote:
> Hi
> I posted my question yesterday regarding the warning about dividing by zero
> and oxygen atoms not being bound to my X atom (P). I have experimented with
> many suggestions and none have worked and I am down to assuming that for
> some reason autogrid does not like the bond lengths of the P-O region and
> therefore treats them as being not bonded. I have mimised this structure so
> I know the bond lengths are reasonable, if i change the X to a C there are
> no problems, if i keep my P as a C and randomly change an oxygen to the X
> atom defining the params in the grid map for P this is accepted too. I have
> found other posts about this but no replies:
> Could somebody please give me some advice. Can these warnings be ignored?
> Is there somewhere I can find the bond lengths for the P(X) - O and
> redefine them?
> I have also experimented with changing the grid center xzy as was suggested
> but for me this maked no difference to the warning message.
> Many thanks, in anticipation of some help!
> Sorry to keep posting so many questions!
> Jo
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> Coventry
> CV4 7AL
> (02476) 574623
> J.F.Hanna at
> ________________________________________________
> --- ADL: AutoDock List  ---
> ---

Boris Gorelik

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 Molecular Modeling and Drug Design Group               
 Department of Medicinal Chemistry and Natural Products 
 School of Pharmacy, Hebrew University of Jerusalem     
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