[Dock-fans] vm_allocate error when loading grid nrg on Intel Mac

Scott Brozell sbrozell at scripps.edu
Wed Sep 5 08:44:23 PDT 2007


Hi,

On Tue, 4 Sep 2007, Francis E Reyes wrote:

> Thanks for the quick reply. Seems like I used a grid.nrg from a PPC
> build. Fixed now.
>
> I'm curious about the anchor and grow step(s). Specifically, will
> clash_overlap prevent the growth of segments/atoms to overlap with
> each other? I only ask this because I did a run with this off, and I
> got molecules which were mostly scrunched up (and scored well).

Yes, see also the use_internal_energy input option in
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFlexibility

> each other? I only ask this because I did a run with this off, and I
> got molecules which were mostly scrunched up (and scored well). Does
> atom overlap get taken care of by the energy minimization step?

Yes, it could assuming that the input options are specified to
not minimize just the anchor; see
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Minimization

Scott

> Thanks
>
> On Sep 4, 2007, at 12:00 PM, Scott Brozell wrote:
>
> > Hi,
> >
> > On Mon, 3 Sep 2007, Francis E Reyes wrote:
> >
> >> I seem to have trouble running dock specifically having trouble
> >> loading my grid nrg file about 26 mb. This is on a Intel Quad Core
> >> Mac with 2 GB of ram. Funny thing is this nrg file works perfectly
> >> well on a PPC build, 1GB of ram.
> >>
> >> mercury 154% cat error.out
> >>
> >> --------------------------------------
> >> DOCK v6.1
> >>
> >> Released December 2006
> >> Copyright UCSF
> >> --------------------------------------
> >>
> >>
> >> Molecule Library Input Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> ligand_atom_file                                             /
> >> private/
> >> var/automount/home/reyesf/dock_TTH_trimer/bin2.mol2
> >> limit_max_ligands                                            no
> >> skip_molecule                                                yes
> >> initial_skip                                                 139
> >> read_mol_solvation                                           no
> >> calculate_rmsd                                               no
> >>
> >> Orient Ligand Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> orient_ligand                                                yes
> >> automated_matching                                           yes
> >> receptor_site_file                                           /
> >> private/
> >> var/automount/home/reyesf/dock_TTH_trimer/selected_spheres.sph
> >> max_orientations                                             100
> >> critical_points                                              no
> >> chemical_matching                                            no
> >> use_ligand_spheres                                           no
> >>
> >> Flexible Ligand Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> 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 Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> bump_filter                                                  yes
> >> bump_grid_prefix                                             /
> >> private/
> >> var/automount/home/reyesf/dock_TTH_trimer/grid
> >> max_bumps_anchor                                             2
> >> max_bumps_growth                                             2
> >>
> >> Master Score Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> score_molecules                                              yes
> >>
> >> Contact Score Paramters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> contact_score_primary                                        no
> >> contact_score_secondary                                      no
> >>
> >> Grid Score Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> grid_score_primary                                           yes
> >> grid_score_secondary                                         no
> >> grid_score_rep_rad_scale                                     1
> >> grid_score_vdw_scale                                         1
> >> grid_score_es_scale                                          1
> >> grid_score_grid_prefix                                       /
> >> private/
> >> var/automount/home/reyesf/dock_TTH_trimer/grid
> >>
> >> Dock3.5 Score Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> dock3.5_score_secondary                                      no
> >>
> >> Continuous Energy Score Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> continuous_score_secondary                                   no
> >>
> >> Zou GB/SA Score Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> gbsa_zou_score_secondary                                     no
> >>
> >> Hawkins GB/SA Score Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> gbsa_hawkins_score_secondary                                 no
> >>
> >> Amber Score Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> amber_score_secondary                                        no
> >>
> >> Warning:  No secondary scoring function selected.
> >>
> >>
> >> Simplex Minimization Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> 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 Typing Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> atom_model                                                   all
> >> vdw_defn_file                                                /
> >> private/
> >> var/automount/home/reyesf/dock6/parameters/vdw_AMBER_parm99.defn
> >> flex_defn_file                                               /
> >> private/
> >> var/automount/home/reyesf/dock6/parameters/flex.defn
> >> flex_drive_file                                              /
> >> private/
> >> var/automount/home/reyesf/dock6/parameters/flex_drive.tbl
> >>
> >> Molecule Library Output Parameters
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >> ligand_outfile_prefix                                        flex
> >> write_orientations                                           no
> >> num_scored_conformers_written                                10
> >> cluster_conformations                                        yes
> >> cluster_rmsd_threshold                                       2
> >> rank_ligands                                                 yes
> >> max_ranked_ligands                                           500
> >> ---------------------------------------------------------------------
> >> ---
> >> ------------------
> >>
> >> Initializing Library File Routines...
> >> Skipped 139 ligands
> >>
> >> Initializing Orienting Routines...
> >> Initializing Conformer Generator Routines...
> >> Initializing Bump Filter Routines...
> >> Reading the bump grid from /private/var/automount/home/reyesf/
> >> dock_TTH_trimer/grid.bmp
> >> Initializing Grid Score Routines...
> >> Reading the energy grid from /private/var/automount/home/reyesf/
> >> dock_TTH_trimer/grid.nrg
> >> Error: memory exhausted!
> >>    For Unix platforms increase the datasize, stacksize, and
> >>    memoryuse using the limit, ulimit, or unlimit commands.
> >> mercury 145% dock6 -i anchor_and_grow.in > error.out
> >> dock6(200) malloc: *** vm_allocate(size=2719518720) failed (error
> >> code=3)
> >> dock6(200) malloc: *** error: can't allocate region
> >> dock6(200) malloc: *** set a breakpoint in szone_error to debug
> >> terminate called after throwing an instance of 'std::bad_alloc'
> >>    what():  St9bad_alloc
> >> Abort
> >> mercury 146%
> >
> > 2719518720 = 2.5GB
> > Are you sure of the details ?
> >
> > How were the grid file(s) generated ?
> > Note that transferring grid files across machines may fail:
> > http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Grid
> >
> > Are both machines 32 bit ?
> > Dock does not fully support 64 bit, but grid has worked for me on
> > 64 bit:
> > http://dock.compbio.ucsf.edu/DOCK_6/faq.htm
> >


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