[Dock-fans] Could not find a valid orientation

[Scott Brozell]

Hi,

On Fri, 13 Mar 2009, Xinyu Guan wrote:

> I have met several problems when I conducted docking.
> First, when I ran dock6, the program stopped spontaneously and the .out file
> said:
> 
> ERROR:  Could not find a valid orientation.
>          (For rigid docking the sought orientation is the whole ligand;
>          for flexible docking the sought orientation is the anchor.)
>          Confirm that all spheres are inside the grid box
> and that the grid box is big enough to contain an orientation.

There are lots of hits on this at
http://dock.compbio.ucsf.edu/DOCK_6/index.htm#searchdockfans
This one is a good place to start:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-November/001280.html

> The second problem is, when I tried to screened out some ligands form a
> large mol2 (contains 1000 zinc ligands), the program would stop with
> 
> Error: memory exhausted!Segmentation fault.

That's not a very large mol2.
All this suggests that something is amiss, such as an unusually large
but askew binding area, etc.
Did you visualize your system at each step of model construction ?
Start small in all aspects and work towards increasing size as necessary.
In particular, this memory error may "fix itself" when your first
problem is resolved.  If not then double check your platform's memory policy:
    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"

Scott