[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


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