[Dock-fans] protein docking segment fault
sbrozell at biomaps.rutgers.edu
Tue Mar 30 20:10:02 PDT 2010
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"
Do the obvious experiment; reduce the grid by half and rerun.
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