[Dock-fans] Fwd: Re: Ligand Docking with DOCK6

Scott Brozell sbrozell at scripps.edu
Tue Apr 8 14:49:00 PDT 2008


Hi,

On Tue, 8 Apr 2008, Francesco Pietra wrote:

> $ ulimit -s unlimited only changed in "ulimit -a" output:
> stack size (k bytes, -s) unlimited
> 
> Under these new conditions, command:
> $ dock6 -i anchor_and_grow_nogrid.in -o anchor_and_grow_nogrid.out
> resulted in a few seconds in:
> 
> terminate called after throwing and instance of 'std::bad_alloc'
>    what (): St9bad_alloc
> Aborted
> 
> During this procedure
> 
> USER        PR  NI  VIRT    RES   SHR    S   CPU   MEM   COMMAND
> francesco  20   0   42048  7476  1448   R    100    0    dock6

Some remaining possibilities are a too big selected_spheres.sph
and a bug.  Please determine the size of the sphere file that
does run with dock6 (and report the memory usage using top) by
systematically reducing selected_spheres.sph.
I ran the continuous score tests using valgrind; there were
no memory problems detected.  A little gooogggling of 
debian std::bad_alloc 
didn't find much.  Naturally you should verify that all the
debian/glib/gcc patches have been applied.

> actually CPU started at 73%, incresed to 100%, then died. I am not sure I understand
> "memory exhausion", though I am sure that during this procedure, memory for dock6
> command did not move from zero.

I assume that the dock output file still contained the memory
exhausted error message.

Scott


> RAM on this machine is large because recently I used to carry out DFT procedures
> with large molecules, recent functionals, and relatively high basis sets.
> 
> The in file was as before:
> 
> ligand_atom_file                                            
> /home/francesco/dockwork/ligand.mol2
> limit_max_ligands                                            no
> skip_molecule                                                no
> read_mol_solvation                                           no
> calculate_rmsd                                               no
> orient_ligand                                                yes
> automated_matching                                           yes
> receptor_site_file                                          
> /home/francesco/dockwork/selected_spheres.sph
> max_orientations                                             1000
> critical_points                                              no
> chemical_matching                                            no
> use_ligand_spheres                                           no
> flexible_ligand                                              yes
> min_anchor_size                                              40
> pruning_use_clustering                                       yes
> pruning_max_orients                                          100
> pruning_clustering_cutoff                                    100
> use_internal_energy                                          yes
> internal_energy_att_exp                                      6
> internal_energy_rep_exp                                      12
> internal_energy_dielectric                                   4.0
> use_clash_overlap                                            no
> bump_filter                                                  no
> score_molecules                                              yes
> contact_score_primary                                        no
> contact_score_secondary                                      no
> grid_score_primary                                           no
> grid_score_secondary                                         no
> dock3.5_score_primary                                        no
> dock3.5_score_secondary                                      no
> continuous_score_primary                                     yes
> continuous_score_secondary                                   no
> cont_score_rec_filename                                     
> /home/francesco/dockwork/protein.mol2
> cont_score_att_exp                                           6
> cont_score_rep_exp                                           12
> cont_score_rep_rad_scale                                     1
> cont_score_use_dist_dep_dielectric                           yes
> cont_score_dielectric                                        4.0
> cont_score_vdw_scale                                         1
> cont_score_es_scale                                          1
> gbsa_zou_score_secondary                                     no
> gbsa_hawkins_score_secondary                                 no
> amber_score_secondary                                        no
> minimize_ligand                                              yes
> minimize_anchor                                              yes
> minimize_flexible_growth                                     yes
> use_advanced_simplex_parameters                              no
> simplex_max_cycles                                           1
> simplex_score_converge                                       0.1
> simplex_cycle_converge                                       1.0
> simplex_trans_step                                           1.0
> simplex_rot_step                                             0.1
> simplex_tors_step                                            10.0
> simplex_anchor_max_iterations                                500
> simplex_grow_max_iterations                                  500
> simplex_final_min                                            no
> simplex_random_seed                                          0
> atom_model                                                   all
> vdw_defn_file                                               
> /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
> flex_defn_file                                              
> /usr/local/dock6/parameters/flex.defn
> flex_drive_file                                             
> /usr/local/dock6/parameters/flex_drive.tbl
> ligand_outfile_prefix                                        flex
> write_orientations                                           no
> num_scored_conformers                                        1
> rank_ligands                                                 no
> 
> Now, with memory slots and HDs from  this machine, and second hand additional
> material, I am trying to assemble an 8 CPUs shared memory (total 24GB). If lucky,
> I'll also have to reinstall the OS and applications. All that in spare time.
> Nevertheless,  succeeding with Dock/Amber with the above large ligands is my primary
> interest at this time.



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