[Dock-fans] bad allocation

[John J. Irwin]

Hi -
How large is the ligand (number of non-H atoms)?
How large are the grid files (any units)?
How many spheres are you using?

Menachem Shoham wrote:
> We are trying to dock a fairly large ligand to a model receptor  
> protein. When I limited the number of spheres, I was able to run a  
> rigid docking program, although the docking score was not very good.  
> When I tried the same thing with flexible docking, it failed with the  
> suggestion of increasing the target area.
> When I increased the number of spheres, the rigid docking failed,  
> giving a message of "-threw instance of std::bad_alloc".
> The grid files are about 10 fold larger than with fewer spheres. Was  
> this due to limitation of our computer or was it due to the large size  
> of the grid files?
>
> 																Barbara Truitt
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>