[Dock-fans] Error: Memory exhausted

Trent E. Balius tbalius at aol.com
Wed Jan 23 08:28:07 PST 2013

 Hi Jagriti,

DOCK and anchor-and-grow is designed to dock small molecules to a protein. 

See the following posting to the dock-fans list for Protein-Protein docking:


I hope this helps,


Trent E. Balius, PhD
Shoichet Lab – Dept. of Pharm Chem,
University of California, San Francisco
           1700 4th Street
           Box 2550
           San Francisco, CA 94158     
Office: Byers Hall, Rm 509
URL: http://docking.org/~tbalius



-----Original Message-----
From: Jagriti Pal <jagriti at mcbl.iisc.ernet.in>
To: dock-fans <dock-fans at docking.org>
Sent: Tue, Jan 22, 2013 9:04 pm
Subject: [Dock-fans] Error: Memory exhausted

---------------------------- Original Message ----------------------------
Subject: Error: Memory exhausted
From:    jagriti at localhost
Date:    Tue, January 22, 2013 1:17 pm
To:      dock-fans at docking.org

Hi all,

I'm trying to dock a 77AA novel protein on another one with known crystal
structure (467 AA). I keep getting the following error when i try to dock
using the anchor and grow method:


Error: memory exhausted!
  If this occurs during grid reading then a likely cause
  is a grid that is too large.  Some machines have a very
  restrictive policy on allocating available resources:
  increase the datasize, stacksize, and memoryuse
  using the limit, ulimit, or unlimit commands;
  for many Linuxes this command sequence will work:
  limit; unlimit; limit
  Otherwise read the man pages or apply trial and error
  to find the apt use of these commands.

terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted (core dumped)


I'm running CentOS 6.3 on a machine having 125gb of ram. I configured dock
using the gnu compiler and did a 'make all' to install the software.

I've tried to dock using 2 box sizes (margin =3 and margin = 5) and with
grid_values between 0.3 and 0.5 but continuously get the same error. Can
anyone help me with this?

Thanks in advance,
Jagriti Pal.
PhD student,
c/o Prof. Kumar Somasundaram
Indian Institute of Science.

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