[Dock-fans] grid problem

David Taylor taylord at hsc.edu
Sat Nov 7 10:40:30 PST 2009


*So I've gotten everything together, and I've attempted to run both rigid
and flex programs, but I keep getting this problem:*

INPUT: molecular at molecular-desktop:~$
/home/molecular/Desktop/dock6/bin/dock6 -i rigid.in -o rigid.out
OUTPUT: terminate called after throwing an instance of 'std::bad_alloc'
                 what():  std::bad_alloc
                 Aborted

*And in the rigid.out file I get this:*

--------------------------------------
DOCK v6.2

Released March 2008
Copyright UCSF
--------------------------------------


Molecule Library Input Parameters
------------------------------------------------------------------------------------------
ligand_atom_file
./1LAH_charged2.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       no

Orient Ligand Parameters
------------------------------------------------------------------------------------------
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file
./selected_spheres.sph
max_orientations                                             1000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no

Flexible Ligand Parameters
------------------------------------------------------------------------------------------
flexible_ligand                                              no

Bump Filter Parameters
------------------------------------------------------------------------------------------
bump_filter                                                  no

Master Score Parameters
------------------------------------------------------------------------------------------
score_molecules                                              yes

Contact Score Parameters
------------------------------------------------------------------------------------------
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                                       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
simplex_max_iterations                                       1000
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_final_min                                            no
simplex_random_seed                                          0

Atom Typing Parameters
------------------------------------------------------------------------------------------
atom_model                                                   all
vdw_defn_file
vdw_AMBER_parm99.defn
flex_defn_file                                               flex.defn
flex_drive_file                                              flex_drive.tbl

Molecule Library Output Parameters
------------------------------------------------------------------------------------------
ligand_outfile_prefix                                        output
write_orientations                                           no
num_scored_conformers                                        10
write_conformations                                          no
cluster_conformations                                        yes
cluster_rmsd_threshold                                       2.0
rank_ligands                                                 no
------------------------------------------------------------------------------------------

Initializing Library File Routines...
Initializing Orienting Routines...
Initializing Grid Score Routines...
 Reading the energy grid from grid.nrg
Error: memory exhausted!
  If this occurs during grid reading then a likely cause
  is a grid that is too large.  Some machines have a very
  restrictive policy on allocating available resources:
  For Unix platforms increase the datasize, stacksize, and
  memoryuse using the limit, ulimit, or unlimit commands;
  use trial and error to find the apt one of these commands.


*So yeah, that's the end of the output. I know this machine has run this
program before, so I must be doing something wrong. I've also tried to
increase stack size and other such things, but that didn't work too well for
me either. Any ideas? Is my input put in wrong so that the computer is doing
a lot of extra work or something?*

*Thanks*
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