[Dock-fans] bus error

Scott Brozell sbrozell at rci.rutgers.edu
Tue May 30 11:45:11 PDT 2017


Hi,

Please use dock-fans at docking.org instead of Dockdev.

On Mon, May 29, 2017 at 05:54:27PM +0200, Urszula Uciechowska wrote:
> 
> after running dock6 -i min.in I am obtaining an error message:
> 
> --------------------------------------
> DOCK v6.7
> 
> Released February 2015
> Copyright UCSF
> --------------------------------------
> 
> 
> Molecule Library Input Parameters
> ------------------------------------------------------------------------------------------
> ligand_atom_file                                             lig_charged.mol2
> limit_max_ligands                                            no
> skip_molecule                                                no
> read_mol_solvation                                           no
> calculate_rmsd                                               yes
> use_rmsd_reference_mol                                       yes
> rmsd_reference_filename                                      lig_charged.mol2
> 
> Database Filter Parameters
> ------------------------------------------------------------------------------------------
> use_database_filter                                          no
> 
> Orient Ligand Parameters
> ------------------------------------------------------------------------------------------
> orient_ligand                                                no
> 
> Internal Energy Parameters
> ------------------------------------------------------------------------------------------
> use_internal_energy                                          yes
> internal_energy_rep_exp                                      12
> Note: Internal energy only includes repulsive VDW for growth and/or
> minimization.
> 
> 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
> 
> MultiGrid Score Parameters
> ------------------------------------------------------------------------------------------
> multigrid_score_secondary                                    no
> 
> Dock3.5 Score Parameters
> ------------------------------------------------------------------------------------------
> dock3.5_score_secondary                                      no
> 
> Continuous Energy Score Parameters
> ------------------------------------------------------------------------------------------
> continuous_score_secondary                                   no
> 
> Descriptor Energy Score Parameters
> ------------------------------------------------------------------------------------------
> descriptor_score_secondary                                   no
> 
> Zou GB/SA Score Parameters
> ------------------------------------------------------------------------------------------
> gbsa_zou_score_secondary                                     no
> 
> Hawkins GB/SA Score Parameters
> ------------------------------------------------------------------------------------------
> gbsa_hawkins_score_secondary                                 no
> 
> SASA Descriptor Score Parameters
> ------------------------------------------------------------------------------------------
> SASA_descriptor_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_tors_premin_iterations                               0
> 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_random_seed                                          0
> simplex_restraint_min                                        yes
> simplex_coefficient_restraint                                10.0
> 
> Atom Typing Parameters
> ------------------------------------------------------------------------------------------
> atom_model                                                   all
> vdw_defn_file                                               
> /home/ares/Software/dock6/parameters/vdw_AMBER_parm99.defn
> flex_defn_file                                              
> /home/ares/Software/dock6/parameters/vdw_AMBER_parm99.defn
> flex_drive_file                                             
> /home/ares/Software/dock6/parameters/flex_drive.tbl
> 
> Molecule Library Output Parameters
> ------------------------------------------------------------------------------------------
> ligand_outfile_prefix                                        lig.min
> write_orientations                                           no
> num_scored_conformers                                        1
> rank_ligands                                                 no
> ------------------------------------------------------------------------------------------
> Bus error
> 
> 
> How to fix it? I am running the tutorial from:
> 
> http://ringo.ams.sunysb.edu/index.php/2017_DOCK_tutorial_1_with_PDB_4QMZ_NEW

This is typically a memory related issue.  Can you build with -g and rerun
to produce a stack trace ?:

cd install; make dockclean; make dock DOCKBUILDFLAGS=' -g '

I am investigating on an Ubuntu platform.

scott



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