[Dock-fans] dock 6 command its saying :aborted <core dumped>

[Scott Brozell]

Hi,

On Sat, 1 Mar 2008, Monisha Hajra wrote:

>     I facing a problem in DOCK in executing dock6 command for a particular
> protein.
> While executing the dock 6 command its saying :aborted <core dumped>
> 
> The message in dock.out file is :
> 
> *Reading the energy grid from grid.nrg
> *>* > Error: memory exhausted!
> *>* >   For Unix platforms increase the datasize, stacksize, and
> *>* >   memorysize using the limit, ulimit, or unlimit commands**l
> 
> 
> I do agree that my ligand my ligand is big, its actually HEM, with two
> chemicals attached with one another , and the grid.nrg file is also
> comparatively large. I am facing this
> problem for particularly this protein. Ant suggestion on how to solve
> this issue ?

Did you try the suggested error recovery  ?

Last time someone posted a message on this error without indicating
whether they tried the suggestion in the message
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-September/001197.html
I expanded the error message;  now in 6.2:
    cout << "Error: memory exhausted!" << endl
        << "  If this occurs during grid reading then a likely cause\n"
        << "  is a grid that is too large.  Some machines have a very\n"
        << "  restrictive policy on allocating available resources:\n"
        << "  For Unix platforms increase the datasize, stacksize, and\n"
        << "  memoryuse using the limit, ulimit, or unlimit commands;\n"
        << "  use trial and error to find the apt one of these commands.\n"

Since your system does seem large, the general approach is to employ
divide and conquer; searching the list will find detailed suggestions:
http://dock.compbio.ucsf.edu/DOCK_6/index.htm

Scott