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

Scott Brozell sbrozell at scripps.edu
Wed Apr 16 23:11:03 PDT 2008


Hi,

On Wed, 16 Apr 2008, Francesco Pietra wrote:

> I got another message from the debian web list:
> 
> >>The std:: would to me make me think C++ namespace 'std' function
> >>'bad_alloc'.  So probably a bad_alloc function exists in C++ and is
> >>returning an error.
> 
> >It is a standard exception thrown when the new() operator fails.
> >Your running out of RAM, perhaps.

Yes.


> >Do you build this program yourself from source?
> 
> Yes, it passed OK all tests, both serial and parallel and it works fine with smaller ligands.
> 
> francesco
> 
> --- On Wed, 4/16/08, Francesco Pietra <chiendarret at yahoo.com> wrote:
> 
> > From: Francesco Pietra <chiendarret at yahoo.com>
> > Subject: Re: Fwd: Re: [Dock-fans] Ligand Docking with DOCK6
> > To: "Scott Brozell" <sbrozell at scripps.edu>
> > Cc: "dock-fans" <dock-fans at docking.org>
> > Date: Wednesday, April 16, 2008, 2:25 PM
> > Hi:
> > Having completed the new machine with 8 logical 875
> > opterons and 24GB memory,  using the same two raid1 HDD
> > (with few adjustments, such as shmmax to 24GB and stack
> > size unlimited) of previous machine, I tried again the flex
> > below. Quickly same error (St9bad_alloc) with (top -i) CPU
> > starting at  100%% and MEM% 0 throughout.
> > 
> > I posted that error message to the debian web list getting
> > a partial answer, that is reported here unabridged:
> > 
> > The std:: would to me make me think C++ namespace
> > 'std' function
> > 'bad_alloc'.  So probably a bad_alloc function
> > exists in C++ and is
> > returning an error.
> > I personally try to avoid dealing with C++ code anymore. 
> > It is get
> > ting
> > too ugly after the STL stuff went in.
> > Try a search for 'C++ bad_alloc' and you will find
> > lots of stuff on
> > bad_alloc in the C++ std library.  About 45000 hits in
> > google.
> > 
> > Is that suggesting anything before I go to investigate
> > systematically the mem% vs. sphere_select dimensions?

No.


> > I recall that with smaller selected_spheres the error
> > message was: Could not complete growth; confirm grid box is
> > large enough   to contain ligand and try increasing
> > max_orients.

With continuous score the grid box does not exist;
it is still possible that max_orientations is too small,
but the value of 1000 makes it very unlikely.

Scott

> > Thanks
> > francesco
> > 
> > 
> > 
> > 
> > --- On Tue, 4/8/08, Scott Brozell
> > <sbrozell at scripps.edu> wrote:
> > 
> > > From: Scott Brozell <sbrozell at scripps.edu>
> > > Subject: Re: Fwd: Re: [Dock-fans] Ligand Docking with
> > DOCK6
> > > To: "Francesco Pietra"
> > <chiendarret at yahoo.com>
> > > Cc: "dock-fans"
> > <dock-fans at docking.org>
> > > Date: Tuesday, April 8, 2008, 2:49 PM
> > > 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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