[Dock-fans] bad allocation

Sudipto Mukherjee sudmukh at yahoo.com
Fri Dec 28 23:17:50 PST 2007

Dear Barbara,

Docking works well with about 50-75
spheres in the binding site. Could you specify how many spheres you are
using? Are all roughly in the binding site? Selecting more spheres
would increase the box size for the grid. The size the grid file
increases roughly as the cube of the box size i.e. proportional to the
volume of the box.

I have tested DOCK successfully with grid
files as large as 800MB on a computer with 2GB RAM . However, if the
grid file is larger than the amount of available memory, memory
allocation errors like the one described is likely.
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
Lab: 631-632-8519, Mobile: 631-220-5744

----- Original Message ----
From: Menachem Shoham <mxs10 at case.edu>
To: dock-fans at docking.org
Sent: Friday, December 28, 2007 12:32:56 AM
Subject: [Dock-fans] bad allocation

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?

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