[Dock-fans] protein docking segment fault

Scott Brozell sbrozell at biomaps.rutgers.edu
Tue Mar 30 20:10:02 PDT 2010


Hi,

On Tue, Mar 30, 2010 at 07:36:29PM -0400, Nicolás Pérez wrote:
> so sorry for not reply, yes I' check the line atom_model changing atom_model
> u to atom_model a and rerun grid command with output  files grid.nrg and
> grid.bmp, to run dock6 with same parameters but I' obtained same errors.
> I' think that the dimensions for grid is the problem, any idea
> 
> El 24 de marzo de 2010 22:01, Nicolás Pérez <
> nicolas.a.perez.barriga at gmail.com> escribió:
> 
> > I' have problem to docking a protein complex, I' try dock  two receptors of
> > cellular surface but I' obtained segment fault when running dock -i
> > rigid.in -o dock.out.
> >  cheking my files dock.out, grid.out, only an dock.out the final message is
> > reading  the energy grid from grid.nrg, I have read mail list dockfans and
> > cheking my dimensions grid, atoms missing and if the spheres inside grid box
> > and appear to be correct.
> > My information grid box
> > Reading in grid box information.
> > Box center of mass                      :   15.970   33.123   60.316
> > Box dimensions                          :   88.996  195.808   68.503
> > Number of grid points per side [x y z]  :      113      246       87
> > Total number of grid points             :  2418426

The grid dimensions are on the large side, but the usual failure for
that is this memory error:

    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"
        << "  increase the datasize, stacksize, and memoryuse\n"
        << "  using the limit, ulimit, or unlimit commands;\n"
        << "  for many Linuxes this command sequence will work:\n"
        << "  limit; unlimit; limit\n"
        << "  Otherwise read the man pages or apply trial and error\n"
        << "  to find the apt use of these commands.\n"
        << endl;

Do the obvious experiment; reduce the grid by half and rerun.

Scott


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