[Dock-fans] bad allocation

Sudipto Mukherjee sudmukh at yahoo.com
Sun Dec 30 21:31:02 PST 2007


Dear Barbara,

If rigid docking works fine with the smaller sphere set (n=84), the grid files are probably fine. 

Flexible docking is a harder sampling problem. Dock quits with the message "Could not complete growth".. etc. when it cannot find any reasonably scored conformation, and this often happens for large, floppy ligands with 7 or more rotatable bonds. In this case, you will have to tweak the sampling parameters in dock. Try disabling the bump filter (this will make docking slower), the clash overlap (may lead to bad ligand conformations), changing the number of orients, min anchor size (=6 is a good idea, but can make things very slow) etc.

Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
----- Original Message ----
From: Barb Truitt <barbara.truitt at case.edu>
To: Sudipto Mukherjee <sudmukh at yahoo.com>
Sent: Monday, December 31, 2007 12:58:06 AM
Subject: Re: [Dock-fans] bad allocation




Sudipto - That may be the problem. I have 354 spheres in the file that I
had tried to run, using a box with 5 angstrom margins. I was able to get
it to run with the tutorial files, and with a smaller cluster of spheres
for our protein that had only 84 spheres, again using a margin of 5
angstroms when forming the box. The grid.nrg files are very large. Is
that because of the number of spheres or because of the characteristics
of our protein? I tried running dock with a smaller selection of spheres,
but it wasn't that much smaller, so the volume of the box wouldn't have
been much smaller. When I ran flexible docking using the smaller number
of spheres, it failed with the suggestion of increasing the size of the
target. I must have overdone it. I'll try again with a smaller number of
spheres. We have ~1.5 GB RAM. How large were your ligands?

Thanks for your help.


Barbara Truitt


At 02:17 AM 12/29/2007, you wrote:

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.

 

Regards

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?


                                                               
Barbara Truitt

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