[Dock-fans] Problems with running the demo for DOCK5

Terry Lang terry at cgl.ucsf.edu
Wed Jul 20 09:24:25 PDT 2005


Dear Aalok,

This line is your problem:

ERROR efopen: Unable to open rec_box.pdb.  Terminating execution.

It means that the accessory programs that run before the grid program did not complete.  Could you run the ./script_clean script and then run the demo again?  One of the first accessory programs cannot write over output files and needs to be cleaned up after before the demo can be run again.  If you are still having problems, can you send me the output again?  Also, what operating system are you using?

Thanks,
Terry 



Aalok Nadkar wrote:

>Dear Terry,
>
>I have attached the output from my demo run of dock5. I had to modify
>( comment out) some of the scripts within the demo directories for the
>output to even get to this point.
>
>I am not sure if it is a problem with my installation or with the
>downloaded files.
>
>Thank you for your help,
>
>Aalok
>
>
>On 7/19/05, Terry Lang <terry at cgl.ucsf.edu> wrote:
>  
>
>>Dear Aalok,
>>
>>          Could you send the output from the demo?  There is something
>>wrong with one of the preprocessing calculations.
>>
>>Sincerely,
>>Terry
>>
>>
>>Aalok Nadkar wrote:
>>
>>    
>>
>>>Dear Sir/Madam,
>>>
>>>
>>>
>>>I am new to using DOCK5. I was trying to run the demo for the Windows
>>>version using Cygwin. It runs fine until it reaches the
>>>
>>>"Initializing Energy Score Routines…" part and then outputs an error message
>>>
>>>
>>>" Could not open ../3_grid/grid.nrg for reading.  Program will terminate"
>>>
>>>
>>>I have tried to see where this file is located or being generated but
>>>have been unsuccessful. Could somebody please assist me in resolving
>>>this issue?
>>>
>>>
>>>Thank you,
>>>
>>>
>>>Aalok Nadkar
>>>
>>>Research Associate
>>>
>>>Chemistry and Biochemistry
>>>
>>>University of Texas at Arlington
>>>_______________________________________________
>>>Dock-fans mailing list
>>>Dock-fans at docking.org
>>>http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>>>
>>>
>>>      
>>>
>>--
>>P. Therese Lang
>>Kuntz and James Labs
>>UCSF--Chemistry and Chemical Biology
>>Phone: (415)476-3986
>>
>>
>>
>>
>>
>>    
>>
>>------------------------------------------------------------------------
>>
>>Generating files that characterize active site
>>Generating files that contain grid energies
>>
>>
>>        UUUUUUU    CCCCCCCC    SSSSSSS/  FFFFFFFFF  
>>      UU/    UU/  CC/    CC/     SS/     FF/    FF/ 
>>     UU/         CCCCCCCC/      SS/     FF/    FF/  
>>    UU/  UUUU/  CC/ CC\        SS/     FF/    FF/   
>>   UU/    UU/  CC/   CC\      SS/     FF/    FF/    
>>   UUUUUUU/   CC/     CC\  SSSSSS/  FFFFFFFFF/      
>>
>>
>>University of California at San Francisco, DOCK 4.0.1
>>
>>__________________Job_Information_________________
>>launch_time                    Wed Jul 20 10:58:46 2005
>>host_name                      unknown
>>memory_limit                   0
>>working_directory              /cygdrive/c/Program Files/DOCK5/dock.5.2_windows/demo/3_grid
>>user_name                      Aalok
>>
>>________________General_Parameters________________
>>compute_grids                  yes
>>grid_spacing                   0.3
>>output_molecule                no
>>
>>________________Scoring_Parameters________________
>>contact_score                  no
>>chemical_score                 no
>>energy_score                   yes
>>energy_cutoff_distance         9999
>>atom_model                     a
>>attractive_exponent            6
>>repulsive_exponent             12
>>distance_dielectric            yes
>>dielectric_factor              4
>>bump_filter                    yes
>>bump_overlap                   0.75
>>
>>____________________File_Input____________________
>>receptor_file                  ../1_struct/rec_charged.mol2
>>box_file                       rec_box.pdb
>>vdw_definition_file            ../../parameters/vdw_AMBER_parm96.defn
>>
>>____________________File_Output___________________
>>score_grid_prefix              grid
>>
>>
>>
>>Reading in coordinates of receptor.
>>CHARGED RESIDUE LYS4                    :    1.000
>>CHARGED RESIDUE LYS10                   :    1.000
>>CHARGED RESIDUE GLU13                   :   -1.000
>>CHARGED RESIDUE GLU14                   :   -1.000
>>CHARGED RESIDUE GLU20                   :   -1.000
>>CHARGED RESIDUE LYS22                   :    1.000
>>CHARGED RESIDUE ASP25                   :   -1.000
>>CHARGED RESIDUE LYS26                   :    1.000
>>CHARGED RESIDUE LYS29                   :    1.000
>>CHARGED RESIDUE ASP30                   :   -1.000
>>CHARGED RESIDUE GLU34                   :   -1.000
>>CHARGED RESIDUE LYS37                   :    1.000
>>CHARGED RESIDUE ASP42                   :   -1.000
>>CHARGED RESIDUE GLU44                   :   -1.000
>>CHARGED RESIDUE LYS45                   :    1.000
>>CHARGED RESIDUE ASP51                   :   -1.000
>>CHARGED RESIDUE LYS59                   :    1.000
>>CHARGED RESIDUE ASP67                   :   -1.000
>>CHARGED RESIDUE LYS69                   :    1.000
>>CHARGED RESIDUE LYS77                   :    1.000
>>CHARGED RESIDUE ARG79                   :    1.000
>>CHARGED RESIDUE ASP82                   :   -1.000
>>CHARGED RESIDUE LYS84                   :    1.000
>>CHARGED RESIDUE ASP89                   :   -1.000
>>CHARGED RESIDUE ASP90                   :   -1.000
>>CHARGED RESIDUE LYS96                   :    1.000
>>CHARGED RESIDUE LYS98                   :    1.000
>>CHARGED RESIDUE ASP101                  :   -1.000
>>CHARGED RESIDUE LYS112                  :    1.000
>>CHARGED RESIDUE GLU115                  :   -1.000
>>CHARGED RESIDUE ARG116                  :    1.000
>>CHARGED RESIDUE GLU120                  :   -1.000
>>CHARGED RESIDUE LYS123                  :    1.000
>>CHARGED RESIDUE GLU124                  :   -1.000
>>CHARGED RESIDUE LYS127                  :    1.000
>>CHARGED RESIDUE ARG128                  :    1.000
>>CHARGED RESIDUE ASP131                  :   -1.000
>>CHARGED RESIDUE LYS133                  :    1.000
>>CHARGED RESIDUE GLU134                  :   -1.000
>>CHARGED RESIDUE GLU144                  :   -1.000
>>CHARGED RESIDUE ASP146                  :   -1.000
>>CHARGED RESIDUE ARG149                  :    1.000
>>CHARGED RESIDUE ARG150                  :    1.000
>>CHARGED RESIDUE ARG151                  :    1.000
>>CHARGED RESIDUE ASP157                  :   -1.000
>>CHARGED RESIDUE LYS160                  :    1.000
>>CHARGED RESIDUE GLU166                  :   -1.000
>>CHARGED RESIDUE LYS167                  :    1.000
>>CHARGED RESIDUE LYS175                  :    1.000
>>CHARGED RESIDUE ASP178                  :   -1.000
>>CHARGED RESIDUE ASP184                  :   -1.000
>>CHARGED RESIDUE GLU195                  :   -1.000
>>CHARGED RESIDUE LYS197                  :    1.000
>>CHARGED RESIDUE ASP206                  :   -1.000
>>CHARGED RESIDUE ARG214                  :    1.000
>>CHARGED RESIDUE GLU217                  :   -1.000
>>CHARGED RESIDUE LYS222                  :    1.000
>>CHARGED RESIDUE ASP225                  :   -1.000
>>CHARGED RESIDUE ASP235                  :   -1.000
>>CHARGED RESIDUE GLU239                  :   -1.000
>>CHARGED RESIDUE LYS242                  :    1.000
>>CHARGED RESIDUE ASP257                  :   -1.000
>>CHARGED RESIDUE LYS262                  :    1.000
>>CHARGED RESIDUE GLU265                  :   -1.000
>>CHARGED RESIDUE LYS273                  :    1.000
>>CHARGED RESIDUE ASP274                  :   -1.000
>>CHARGED RESIDUE GLU276                  :   -1.000
>>CHARGED RESIDUE LYS279                  :    1.000
>>CHARGED RESIDUE GLU282                  :   -1.000
>>CHARGED RESIDUE ASP285                  :   -1.000
>>CHARGED RESIDUE ARG291                  :    1.000
>>CHARGED RESIDUE ASP292                  :   -1.000
>>CHARGED RESIDUE LYS295                  :    1.000
>>CHARGED RESIDUE GLU296                  :   -1.000
>>CHARGED RESIDUE GLU297                  :   -1.000
>>CHARGED RESIDUE GLU299                  :   -1.000
>>CHARGED RESIDUE LYS300                  :    1.000
>>CHARGED RESIDUE LYS301                  :    1.000
>>
>>Total charge on ****                    :   -4.000
>>
>>Reading in grid box information.
>>ERROR efopen: Unable to open rec_box.pdb.  Terminating execution.
>>Performing DOCK run
>>
>>
>>
>>--------------------------------------
>>DOCK v5.2.0-Beta
>>
>>Released March 2005
>>Copyright UCSF
>>Authored by:
>>	Tack Kuntz
>>	Demetri Moustakas
>>	Paula Therese Lang
>>	Scott Pegg
>>--------------------------------------
>>
>>
>>Molecule Library Parameters
>>------------------------------------------------------------------------------------------
>>ligand_atom_file                                             ../1_struct/lig_charged.mol2
>>ligand_outfile_prefix                                        lig
>>limit_max_ligands                                            no
>>write_orientations                                           no
>>write_conformations                                          no
>>initial_skip                                                 0
>>calculate_rmsd                                               yes
>>use_rmsd_reference_mol                                       no
>>rank_ligands                                                 no
>>num_scored_poses_written                                     1
>>
>>Orient Ligand Parameters
>>------------------------------------------------------------------------------------------
>>orient_ligand                                                yes
>>automated_matching                                           yes
>>receptor_site_file                                           ../2_site/sphgen_cluster.sph
>>max_orientations                                             500
>>critical_points                                              no
>>chemical_matching                                            no
>>use_ligand_spheres                                           no
>>
>>Flexible Ligand Parameters
>>------------------------------------------------------------------------------------------
>>flexible_ligand                                              yes
>>
>>Anchor & Grow Parameters
>>------------------------------------------------------------------------------------------
>>ag_conf_search                                               yes
>>min_anchor_size                                              50
>>num_anchor_poses                                             50
>>number_confs_per_cycle                                       50
>>use_internal_energy                                          yes
>>internal_energy_att_exp                                      6
>>internal_energy_rep_exp                                      12
>>internal_energy_dielectric                                   4.0
>>use_clash_overlap                                            no
>>
>>Bump Filter Parameters
>>------------------------------------------------------------------------------------------
>>bump_filter                                                  no
>>
>>Master Score Parameters
>>------------------------------------------------------------------------------------------
>>score_molecules                                              yes
>>
>>Energy Score Parameters
>>------------------------------------------------------------------------------------------
>>energy_score_primary                                         yes
>>energy_score_secondary                                       yes
>>vdw_scale                                                    1
>>es_scale                                                     1
>>nrg_grid_prefix                                              ../3_grid/grid
>>
>>Simplex Minimization Parameters
>>------------------------------------------------------------------------------------------
>>minimize_ligand                                              yes
>>minimize_anchor                                              yes
>>minimize_flexible_growth                                     yes
>>minimize_final_pose                                          yes
>>use_advanced_simplex_parameters                              no
>>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_anchor_min_max_iterations                            50
>>simplex_flex_min_max_iterations                              10
>>simplex_final_min_max_iterations                             100
>>simplex_random_seed                                          0
>>
>>Atom Typing Parameters
>>------------------------------------------------------------------------------------------
>>atom_model                                                   all
>>vdw_defn_file                                                ../../parameters/vdw_AMBER_parm96.defn
>>flex_defn_file                                               ../../parameters/flex.defn
>>flex_drive_file                                              ../../parameters/flex_drive.tbl
>>chem_defn_file                                               ../../parameters/chem.defn
>>------------------------------------------------------------------------------------------
>>
>>Initializing Library File Routines...
>>Initializing Orienting Routines...
>>Initializing Conformer Generator Routines...
>>Initializing Energy Score Routines...
>>
>>
>>Could not open ../3_grid/grid.nrg for reading.  Program will terminate.
>>
>>    
>>

-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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