[Dock-fans] Fwd: generatin Sphere failure

[Scott Brozell]

Hi,

On Fri, 19 Oct 2007, Francesco Pietra wrote:

> I solved the problem with Andrew Magis' sphgen_cpp 

Good.  Since you later indicated that there were
118807 surface points in 91 clusters,
it is likely that the five digit restriction on the number of spheres
caused the error when reading the intermediate file temp2.

The incorrect (9999) restriction on the number of spheres in
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
has been corrected and will be posted soon.

Scott

> --- Francesco Pietra <chiendarret at yahoo.com> wrote:
> 
> > Date: Thu, 18 Oct 2007 09:38:37 -0700 (PDT)
> > From: Francesco Pietra <chiendarret at yahoo.com>
> > Subject: generating Sphere failure
> > To: dock-fans <dock-fans at docking.org>
> > 
> > I carried out successfully all DOCK6.1 tutorials. In contrast, when I tried
> > to
> > apply the defaults of the tutorials to a large protein (an ion channel
> > teepee),
> > I met failure at the Generating Spheres stage.
> > 
> > Command "sphgen" generated an empty teepee_noH.sph  file (the requested file
> > in
> > INSPH), alongside temp1.ms temp2.sph temp3.atc files. The error is
> > illustrated
> > in OUTSPH:
> > 
> > density type = X
> >  reading  teepee_noH.ms                                                      
> >  
> >          type   R
> >  # of atoms =   3412   # of surf pts =  *****
> >  finding spheres for   teepee_noH.ms                                         
> >  
> >                    
> >  dotlim =     0.000
> >  radmax =    4.000
> >  Minimum radius of acceptable spheres?
> >   1.39999998
> >  output to  teepee_noH.sph                                                   
> >  
> >         
> >  error reading temp2.sph
> >     0   89  1.4954  100457    0.011160   25.497364   11.149721  -10.546585
> > 
> > 
> > There are no "# of surf pts" and "temp2.sph" could not be read. Was that due
> > to
> > a too large protein or to unsuited defaults of the tutorial? Also, are the
> > temp.* files intermediate files during the computation? (they were not
> > present
> > at completed tutorial). I can't imagine if this is sufficient information for
> > a
> > rough diagnosis. It is the first time I move outside the tutorials with DOCK.