[Dock-fans] Re: a problem while running flexible DOCKing

Scott Brozell sbrozell at scripps.edu
Mon Mar 19 10:39:22 PST 2007


Hi,

> Do I need to define anchor atoms and rigid
> bonds for each molecules before flexible docking?

In general, no.
However, See the 'Identification of Rigid Segments' section of the
manual for reasons why one might want to make more bonds rigid.
See the 'Manual Specification of Non-rotatable Bonds' section of the
manual for how to make more bonds rigid.

These are in this section
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFlexibility

Scott

---------- Forwarded message ----------
Date: Wed, 14 Mar 2007 15:35:31 -0400
From: Youyi Peng <pengyo at umdnj.edu>
Subject: Re: a problem while running flexible DOCKing

Hi John,
Thanks a lot.
Actually, my molecules are not that big. They have 30 and 18 heavy
atoms. I succeeded in docking a 23-heavy atom molecule with the same
spheres and input files. Do I need to define anchor atoms and rigid
bonds for each molecules before flexible docking?
By th way, my target is a kinase. My system is Linux.

Regards,

Youyi

----- Original Message -----
From: "John J. Irwin"
Date: Wednesday, March 14, 2007 2:53 pm
Subject: Re: a problem while running flexible DOCKing

> Hi Youyi
>
> D is for Dalton, thus under 250 D means fragments. If fragments
> dock,
> your spheres are probably fine. So you seem to be having a big
> molecule
> problem. How big are your molecules?
>
> There has been some discussion of "Could not complete growth", but
> I don't remember whether there was a bugfix or not.
>
>
> Youyi Peng wrote:
> > Hi John,
> > When I run flexible docking with DOCK6, I got the following error
> message:> ERROR:  Could not complete growth.
> >          Confirm grid box is large enough to contain
> >          ligand and try increasing max_orients.
> >
> > I searched DOCK-FAN archives and found your solution for it.
> > 1. Do you have a small binding site? Perhaps the molecules are
> too big
> > to fit?
> > 2. Are the spheres in the correct location?
> > 3. Try docking small molecules (e.g. benzoic acid, aniline). Do
> they fit?
> > 4. If yes to 3, try again around 250 D. If no to 3, I suspect
> there is
> > something very obviously wrong - did you look at the structure?
> >
> > My case is YES to 3. What do you mean in 4? What is "250 D"?
> > By the way, I increased max_orients to 1000 but still get this
> error.>
> > Thank you very much!


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