[Dock-fans] vm_allocate error when loading grid nrg on Intel Mac
Francis E Reyes
Francis.Reyes at Colorado.EDU
Mon Sep 3 21:23:58 PDT 2007
Hi all
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.
I have enclosed the log below.
Thanks for any advice
FR
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%
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070903/5b581268/attachment-0001.html
More information about the Dock-fans
mailing list