[Dock-fans] chemical_matching seg fault

Scott Brozell sbrozell at scripps.edu
Wed Mar 14 13:38:16 PST 2007


Hi,

Thank you for your report.
We shall investigate your problem.

Scott

> On Wed, 14 Mar 2007 16:01:27 +0100 Maria Miteva wrote:
>
> I am trying to use the chemical match in DOCK6. However after several
> molecules DOCK6  stops with Segmentation fault.
>
> With the same parameters and input files  with Manual match and without
> Chemical match I have not any problems.
>
> Can you help me, please,  to resolve the problem with Chemical matching?
>
> Enclose you can find my input parameters file and the sph file.


ligand_atom_file                    /home/maria/diverset_2004_3DDOCK/diverset_march2004_F_very_very_light_xad_3DDOCK_5_50_50conf_conformers.mol2
ligand_outfile_prefix               NA_Diver3DDock_ad_contact_Dock6_or500_p30_075_sph
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                  no
distance_tolerence                  0.25
distance_minimum                    2.0
nodes_minimum                       3
nodes_maximum                       10
receptor_site_file                  ../2_site/final_chemical.sph
max_orientations                    500
critical_points                     no
chemical_matching                   yes
chem_match_tbl                      /usr/local/programs/DOCK/dock6/parameters/chem_match.tbl
use_ligand_spheres                  no
flexible_ligand                     no
bump_filter                         yes
bump_grid_prefix                    ../3_grid/grid_chem_075
max_bumps                           8
score_molecules                     yes
contact_score_primary               yes
contact_score_secondary             yes
contact_score_cutoff_distance       4.5
contact_score_clash_overlap         0.75
contact_score_clash_penalty         30.0
contact_score_grid_prefix           ../3_grid/grid_chem_075
minimize_ligand                     no
atom_model                          all
vdw_defn_file                       /usr/local/programs/DOCK/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file                      /usr/local/programs/DOCK/dock6/parameters/flex.defn
flex_drive_file                     /usr/local/programs/DOCK/dock6/parameters/flex_drive.tbl
chem_defn_file                      /usr/local/programs/DOCK/dock6/parameters/chem.defn


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