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

Francesco Pietra chiendarret at yahoo.com
Mon Apr 21 14:10:59 PDT 2008



--- On Mon, 4/21/08, Scott Brozell <sbrozell at scripps.edu> wrote:

> From: Scott Brozell <sbrozell at scripps.edu>
> Subject: Re: [Dock-fans] Fw: Re: Fw: Re: Fwd: Re:  Ligand Docking with DOCK6
> To: "Francesco Pietra" <chiendarret at yahoo.com>
> Cc: "dock-fans" <dock-fans at docking.org>
> Date: Monday, April 21, 2008, 1:30 PM
> Hi,
> 
> On Mon, 21 Apr 2008, Francesco Pietra wrote:
> 
> > Good news, I hope. Please see below. A quick response
> would be much appreciated in order to decide whether to
> continue or stop the calculation.  Thanks, francesco pietra
> > 
> > --- On Thu, 4/17/08, Scott Brozell
> <sbrozell at scripps.edu> wrote:
> > 
> > > First priority is to investigate
> selected_spheres.sph.
> > > 
> > > Scott
> > 
> > With my new machine (NUMA-type 4 dual-opteron 875 for
> a total 8 logical CPUs, 23GB mem + 1GB for debian linux
> amd6a) I am carrying out a flex docking on the same large
> ligand where (with previous machine, 2 dual-opteron, 15GB
> available mem) memory exhausion occurred both on grid and
> continuous score (selected_spheres.sph was derived from a
> radius 25A - comprising 10,536,750 grid points, in a 37088
> b file. In all cases (also below) stack size unlimited.
> > 
> > Now, setting a 23A radius, selected_spheres totals
> 7,675,200 points in a 30770 bytes file. A flex docking
> (serial, see below the same *.in file for the above
> unsuccessful runs) is going on. Top (dock6 command) showed
> %CPU starting at 0, then rapidly 25, then 100. %Mem started
> at 0, the, in 10 min 28%, reaching 29.4% (i.e., 7474212
> used). The situation is now:
> > 
> > PID (3744), USER (f), PR (25), NI (0), VIRT (7112m),
> RES (6.8g), SHR (1624), S (R), %CPU (100), %MEM (29.4),
> TIME+ (1624), COMMAND (dock6).
> > 
> > Nothing is being further written  to either the *.out
> file or the *.mol2 file. The latter is zero bytes, the
> former 6668 b, staying at what was initially written; end
> lines read:
> > 
> > Initialing Library File Routines ...
> > Initializing Orienting Routines ...
> > Initializing Conformer Generator Routines...
> > 
> > *.in file:
> > 
> > ligand_atom_file                                      
>       /home/francesco/dockwork/ctx3c_flex_dock62/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/ctx3c_flex_dock62/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/ctx3c_flex_dock62/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
> > _____________________-
> > 
> > Should the computation be completed? It would be no
> time loss as I am interested to go on with this ligand,
> though I am worried by not having any indications about the
> trend of energy. Apparently there is access to disk: is any
> temp file written?
> > 
> 
> Probably.  It looks like selected_spheres.sph was too big:
> 23A gives 7,675,200 points and yields about 7GB memory
> consumption.
> 25A gives 10,536,750 points and yields more than 15/2GB


Actually more than 23G I tried on the new machine too.

> memory consumption.
> There are no temporary files.
> If you are uneasy then try a much smaller calculation for
> verification
> and benchmarking.
> 


Leave running overnight present job (now the top indication is as above, except for TIME+ 2096. Tomorrow, if still running without writing anything else to the *.out file, i.e., without any indication where the calculation is, I'll kill the job and retry in parallel.

As to grid scoring, spheres.sph 23A 7,675,200 points (corresponding to box 8A), provided no room enough for the ligand, according to message of failure of the flex run.

Thanks
francesco
> Scott


      ____________________________________________________________________________________
Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ


More information about the Dock-fans mailing list