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

Scott Brozell sbrozell at scripps.edu
Mon Apr 21 13:30:09 PDT 2008


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

Scott




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