[Dock-fans] failure on dock.mpi

Alessandro Nascimento al.s.nascimento at gmail.com
Mon Jul 9 10:16:54 PDT 2007


Hi dock users,

I'm new to dock and also to molecular docking...

I took a look at the tutorials, and I am trying to do my first dock
using a database (zinc).
When running dock in a single processor, my job works fine. When I try
it in parallel (5 processors, mpich2), i get the following error

[cli_1]: rank 0 in job 8  ruska_37276   caused collective abort of all ranks
  exit status of rank 0: killed by signal 11

I pasted my dock input file below. Any clue to this problem?



ligand_atom_file                                             zinc.mol2
limit_max_ligands                                            yes
max_ligands                                                  100
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           rec.sph
max_orientations                                             120000
critical_points                                              yes
chemical_matching                                            yes
chem_match_tbl
/home/apps/dock/dock6/parameters/chem_match.tbl
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_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       grid
dock3.5_score_secondary                                      no
continuous_score_secondary                                   yes
cont_score_rec_filename                                      rec_charged.mol2
cont_score_att_exp                                           6
cont_score_rep_exp                                           12
cont_score_rep_rad_scale                                     1
cont_score_dielectric                                        4.0
cont_score_vdw_scale                                         1
cont_score_es_scale                                          1
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_secondary_minimize_pose                              yes
use_advanced_secondary_simplex_parameters                    no
simplex_secondary_max_iterations                             100
simplex_secondary_min_add_internal                           no
simplex_random_seed                                          0
atom_model                                                   all
vdw_defn_file
/home/apps/dock/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file
/home/apps/dock/dock6/parameters/flex.defn
flex_drive_file
/home/apps/dock/dock6/parameters/flex_drive.tbl
chem_defn_file
/home/apps/dock/dock6/parameters/chem.defn
ligand_outfile_prefix                                        flex
write_orientations                                           no
num_primary_scored_conformers_rescored                       4
cluster_primary_conformations                                yes
cluster_rmsd_threshold                                       2.0
num_clusterheads_for_rescore                                 5
num_secondary_scored_conformers_written                      4
rank_primary_ligands                                         no
max_primary_ranked                                           10
rank_secondary_ligands                                       no
max_secondary_ranked                                         10

-- 
[ ]s

--alessandro


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