Dock I/O Files

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[A]. "grid" program:
 %  grid -i grid.in

(grid.in contents)


INPUT FILES: 
  1. receptor_file - Receptor/Protein 3D structure: ece.mol2 
  2. box_file - box.pdb 
  3. vdw_definition_file            parameter/vdw.defn
  4. chemical_definition_file       parameter/chem.defn

OUTPUT FILES:
  1. four output files: ece.bmp  ece.chm  ece.cnt  ece.nrg
     (output file stored in local or different directory
      depending settings of score_grid_prefix.)
  2. receptor_out_file              ece_out.mol2

Assuming seeting in input file grid.in contain:
  1. score_grid_prefix              dock_inputs/ece
  2. receptor_out_file              ece_out.mol2

Output Message of program run
NOTE: The output files of dock "grid" program produces binary
files. That means, they are NOT portable to different architectures. Because
you may encounter problems such as little/big-endian and different datasize
(binary data produced on 32-bit system cann't be moved to 64-bit system).
Therefore, if you Grid resources are running different OSes/Arch, then
you need to perform "docking grid" on each class of machine. And then
prestage these files on appropriate remote machines. For example, if
you have produced docking grid outfiles on SunOS, then you can use
those binary files as inputfiles to "dock" program on all resources
that are running SunOS operating system.

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[B] "dock" program:

 % dock -i dock.in  -o dock_out

(parameteruzed dock.in file contents. the actual "dock.in" will
be created through substitution by Nimrod-G at runtime)

INPUT FILES:

 0. dock.in -- a configuration file
 1. output files of "grid" program -- ece.bmp  ece.chm  ece.cnt  ece.nrg
    (In dock.pln or dock.in there is parameter score_grid_prefix with value "ece")

 2. receptor_site_file: "ece.sph" -- which is output of "sphgen" program.
 
 3. vdw_definition_file            vdw.defn
 4. chemical_definition_file       chem.defn
 5. chemical_score_file            chem_score.tbl
 6. flex_definition_file           flex.defn
 7. flex_drive_file                flex_drive.tbl
 8. ligand_atom_file:               ${ligand_number}.mol2
   (this file contain molecule record extracted by "get_molecule" client using
   services of the the CDB server")

OUTPUT FILES:

1. dock_out
2. ligand_contact_file            dock_cnt.mol2
3. ligand_chemical_file           dock_chm.mol2
4. ligand_energy_file             dock_nrg.mol2
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