[Dock-fans] Fwd: generatin Sphere failure

[Francesco Pietra]

I solved the problem with Andrew Magis' sphgen_cpp 

francesco

--- 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.
> 
> Thanks
> 
> francesco pietra
> 
> 
> 
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