[Dock-fans] bad allocation

Menachem Shoham mxs10 at case.edu
Thu Dec 27 11:02:56 PST 2007

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

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