[Dock-fans] protein docking segment fault

Nicolás Pérez nicolas.a.perez.barriga at gmail.com
Tue Mar 30 16:36:29 PDT 2010


OOOH,

so sorry for not reply, yes I' check the line atom_model changing atom_model
u to atom_model a and rerun grid command with output  files grid.nrg and
grid.bmp, to run dock6 with same parameters but I' obtained same errors.
I' think that the dimensions for grid is the problem, any idea

thanks

El 24 de marzo de 2010 22:01, Nicolás Pérez <
nicolas.a.perez.barriga at gmail.com> escribió:

> 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:
> grid.in
> 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
> vdw_definition_file
> /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
> 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
> vdw_defn_file
> /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
> flex_defn_file
> /usr/local/dock6/parameters/flex.defn
> flex_drive_file
> /usr/local/dock6/parameters/flex_drive.tbl
>
> what is wrong?
>
> --
> Nicolás Pérez Barriga
>
> Estudiante Pregrado
> Ingeniería Bioprocesos
> Escuela Ingeniería Bioquímica
> Pontíficia Universidad Católica de Valparaíso
>



-- 
Nicolás Pérez Barriga

Estudiante Pregrado
Ingenieria Bioprocesos
Escuela Ingenieria Bioquimica
Pontíficia Universidad Católica de Valparaíso
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