[Dock-fans] Problem in Grid stage...........

[Scott Brozell]

Hi,

On Wed, 21 May 2008, raghu bhagavat wrote:

> i am new to Dock processing...........i am followin the tutorials and am
> encountering a problem in Grid.........
> 
> vdw_definition_file            ../../../parameters/vdw_AMBER_parm99.defn
> this file i am not able to find and in my grid.out file i am findin an error like this:
> _File_Input____________________
> receptor_file                  /home/allinone/samta/dms/rec_charged.mol2
> box_file                       rec_box.pdb
> ERROR get_parameter: Unable to get value for vdw_definition_file parameter.

It works for me; see below.
If you have your grid.in in an unusual location then modify the
vdw_definition_file accordingly.

Scott

% pwd
/dock/dock6/tutorials/ligand_sampling_demo/3_grid
% ll ../../../parameters/vdw_AMBER_parm99.defn
12 -rw-r--r-- 1 rppl 9493 Feb 29 16:45 ../../../parameters/vdw_AMBER_parm99.defn
%  ./script_demo

        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                    Thu May 22 17:41:10 2008
host_name                      opt-login01.osc.edu
memory_limit                   1073741824
working_directory              /home/srb/dock/dock6/tutorials/ligand_sampling_demo/3_grid
user_name                      srb

________________General_Parameters________________
compute_grids                  yes
grid_spacing                   0.3
output_molecule                no

________________Scoring_Parameters________________
contact_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_parm99.defn

____________________File_Output___________________
score_grid_prefix              grid

...



% pwd
/dock/dock6/tutorials/mpi_demo/3_grid
% ll ../../../parameters/vdw_AMBER_parm99.defn
12 -rw-r--r-- 1 rppl 9493 Feb 29 16:45 ../../../parameters/vdw_AMBER_parm99.defn
%  ./script_demo

        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                    Thu May 22 17:39:10 2008
host_name                      opt-login01.osc.edu
memory_limit                   1073741824
working_directory              /home/srb/dock/dock6/tutorials/mpi_demo/3_grid
user_name                      srb

________________General_Parameters________________
compute_grids                  yes
grid_spacing                   0.3
output_molecule                no

________________Scoring_Parameters________________
contact_score                  no
energy_score                   yes
energy_cutoff_distance         9999
atom_model                     a
attractive_exponent            6
repulsive_exponent             9
distance_dielectric            yes
dielectric_factor              4
bump_filter                    yes
bump_overlap                   0.75

____________________File_Input____________________
receptor_file                  ../1_struct/1VRT.rec.mol2
box_file                       rec_box.pdb
vdw_definition_file            ../../../parameters/vdw_AMBER_parm99.defn

____________________File_Output___________________
score_grid_prefix              1VRT.rec

...