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

Francesco Pietra chiendarret at yahoo.com
Mon Apr 21 01:46:54 PDT 2008

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:

> 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: Thursday, April 17, 2008, 11:59 PM
> Hi,
> 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?




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