[Dock-fans] vm_allocate error when loading grid nrg on Intel Mac
Scott Brozell
sbrozell at scripps.edu
Tue Sep 4 11:00:07 PDT 2007
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
Scott
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