[Dock-fans] protein docking segment fault

Nicolás Pérez nicolas.a.perez.barriga at gmail.com
Wed Mar 24 19:01:59 PDT 2010

Dear dock6 users,

I' have problem to docking a protein complex, I' try dock  two receptors of
cellular surface but I' obtained segment fault when running dock -i
rigid.in-o dock.out.
 cheking my files dock.out, grid.out, only an dock.out the final message is
reading  the energy grid from grid.nrg, I have read mail list dockfans and
cheking my dimensions grid, atoms missing and if the spheres inside grid box
and appear to be correct.
My information grid box
Reading in grid box information.
Box center of mass                      :   15.970   33.123   60.316
Box dimensions                          :   88.996  195.808   68.503
Number of grid points per side [x y z]  :      113      246       87
Total number of grid points             :  2418426
My files configuration:
compute_grids                  yes
grid_spacing                   0.8
output_molecule                no
contact_score                  no
energy_score                   yes
energy_cutoff_distance         9999
atom_model                     u
attractive_exponent            6
repulsive_exponent             12
distance_dielectric            yes
dielectric_factor              4
bump_filter                    yes
bump_overlap                   0.75
receptor_file                  bmp1ar.mol2
box_file                       box6.pdb
score_grid_prefix              grid

My file dock rigid.in:
ligand_atom_file                                             bmp1br.2.mol2
ligand_outfile_prefix                                        rigid
limit_max_ligands                                            no
read_mol_solvation                                           no
write_orientations                                           no
write_conformations                                          no
skip_molecule                                                no
calculate_rmsd                                               no
rank_ligands                                                 no
num_scored_conformers_written                                1
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           bmp1ar_noH.sph
max_orientations                                             1000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
flexible_ligand                                              no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       grid
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
amber_score_secondary                                        no
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_add_internal                               no
simplex_random_seed                                          0
atom_model                                                   all

what is wrong?

Nicolás Pérez Barriga

Estudiante Pregrado
Ingeniería Bioprocesos
Escuela Ingeniería Bioquímica
Pontíficia Universidad Católica de Valparaíso
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