[Dock-fans] protein docking segment fault

Nicolás Pérez nicolas.a.perez.barriga at gmail.com
Sat Mar 27 15:39:02 PDT 2010


Hi,

I`check every file, but all is correct. My protein models are homology
models, having special formatting for this models?

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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