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

[Scott Brozell]

Hi,

> > > *>* >   For Unix platforms increase the datasize, stacksize, and
> > > *>* >   memorysize using the limit, ulimit, or unlimit commands

vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> > Did you try the suggested error recovery  ?
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

You still did not indicate if you tried those limit commands.

Scott

On Fri, 14 Mar 2008, Monisha Hajra wrote:

>    I did tried with making small grid box , I had minimized the grid box
> upto 3A radius compared  to usual 10A radius. Still its showing the same
> result. What else I can try ?
> 
> Thanks
> Monisha
> 
> On Fri, Mar 14, 2008 at 8:34 AM, Scott Brozell <sbrozell at scripps.edu> wrote:
> 
> > 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