[Dock-fans] Fwd: Large ligand on Large grid Kill mpirun

Francesco Pietra chiendarret at yahoo.com
Fri Nov 16 02:18:15 PST 2007


I forgot an important observation: docking procedures went on regularly even
for the largest (155 and 165 atoms) ligands when, on previous runs, the spheres
covered ca 1/4 of the protein.

--- Francesco Pietra <chiendarret at yahoo.com> wrote:

> Date: Fri, 16 Nov 2007 02:11:22 -0800 (PST)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Large ligand on Large grid Kill mpirun
> To: dock-fans <dock-fans at docking.org>
> 
> Following careful comparative runs I arrived at the conclusion that too large
> ligands on large grids kill mpirun. 
> 
> With grid files and selected_spheres.sph (10,536,750 grid points), for
> ligands
> of 118 atoms, or less, docking and amber rescore procedures went to
> completion
> OK. Selected spheres was centered (Magis' sphere_select) symmetrically in the
> protein for a 25A radius, whereby the spheres covered most of the protein.
> 
> mpirun failure occurred with two ligands of much similar shape as above
> though
> larger (155 atoms and 165 atoms)
> 
> 
> How mpirun was killed shortly after launching the rigid score procedure, is
> shown by outputting the screen events following "mpirun -np 4 -i rigid.in -o
> rigid.out 2>&1 | tee screen.out":
> 
> Initializing MPI Routines...
> Initializing MPI Routines...
> Initializing MPI Routines...
> Initializing MPI Routines...
> terminate called after throwing an instance of 'std::bad_alloc'
>   what():  St9bad_alloc
> [deb64:03725] *** Process received signal ***
> [deb64:03725] Signal: Aborted (6)
> [deb64:03725] Signal code:  (-6)
> [deb64:03725] [ 0] /lib/libpthread.so.0 [0x2b21e08e0410]
> [deb64:03725] [ 1] /lib/libc.so.6(gsignal+0x3b) [0x2b21e0a1807b]
> [deb64:03725] [ 2] /lib/libc.so.6(abort+0x10e) [0x2b21e0a1984e]
> [deb64:03725] [ 3]
> /usr/lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x114)
> [0x2b21e0583424]
> [deb64:03725] [ 4] /usr/lib/libstdc++.so.6 [0x2b21e05815a6]
> [deb64:03725] [ 5] /usr/lib/libstdc++.so.6 [0x2b21e05815d3]
> [deb64:03725] [ 6] /usr/lib/libstdc++.so.6 [0x2b21e05816ba]
> [deb64:03725] [ 7] dock6.mpi(main+0) [0x42c180]
> [deb64:03725] [ 8] /usr/lib/libstdc++.so.6(_Znwm+0x34) [0x2b21e0581954]
> [deb64:03725] [ 9] /usr/lib/libstdc++.so.6(_Znam+0x9) [0x2b21e0581a49]
> [deb64:03725] [10] dock6.mpi(_ZN6Orient12match_ligandER7DOCKMol+0x375)
> [0x447a85]
> [deb64:03725] [11] dock6.mpi(main+0xaf5) [0x42cc75]
> [deb64:03725] [12] /lib/libc.so.6(__libc_start_main+0xda) [0x2b21e0a054ca]
> [deb64:03725] [13] dock6.mpi(__gxx_personality_v0+0xc2) [0x41b4ea]
> [deb64:03725] *** End of error message ***
> mpirun noticed that job rank 0 with PID 3724 on node deb64 exited on signal
> 15
> (Terminated). 
> 3 additional processes aborted (not shown).
> 
> File rigid.out showed correct reading of grid.nrg.
> 
> _______
> The procedure failed also on serial run with 
> 
> dock6 -i rigid.in -o rigid.out 2>&1 screen_serial.out
> 
> screen_serial.out:
> 
> terminate called after throwing an instance of 'std::bad_alloc'
> waht(): St9bad_alloc
> 
> 
> i.e, as it was already clear from the above, not a problem of mpi.
> 
> ______
> 
> I understand to be largely out of the main stream of docking procedures (and
> probably scope). Nonetheless, I am interested in how these large ligands
> behave. Therefore, how could I manage to compare the above ligands of various
> size?. I am wondering about changing the grid space and see if docking with
> the
> smaller ligands changes much or not. If OK I could try the larger ligands
> with
> the new grid. Any better idea? I am not considering to work without a grid
> because I want to compare several molecules. So far I used defaults from
> tutorials, i.e. for grid.in:
> 
> compute_grids                  yes
> grid_spacing                   0.3
> output_molecule                no
> contact_score                  no
> energy_score                   yes
> energy_cutoff_distance         9999
> atom_model                     a
> attractive_exponent            6
> repulsive_exponent             12
> distance_dielectric            yes
> dielectric_factor              4
> bump_filter                    yes
> bump_overlap                   0.75
> receptor_file    /home/francesco/dockwork/grid/myprotein.mol2
> box_file            /home/francesco/dockwork/grid/rec_box.pdb
> vdw_definition_file /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
> score_grid_prefix              grid
> 
> 
> All that was carried out using A. Magis' sphgen_cpp and sphere_select.
> 
> Thanks
> 
> francesco pietra
> ________________
> 
> 
> 
> 
> 
> 
>      
>
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