[Dock-fans] Docking Experiment by DOCK6.4

lsoltang at uwaterloo.ca lsoltang at uwaterloo.ca
Wed Jul 27 12:39:27 PDT 2011



Hello.

I'm a beginner with the DOCK software. I've performed a docking  
experiment following the instructions in the manual: anchor-and-grow,  
energy-based grid, etc.
The last part of the output is as follows:

----------------------------------------------------------
Initializing Library File Routines...
Initializing Orienting Routines...
Initializing Conformer Generator Routines...
Initializing Grid Score Routines...
  Reading the energy grid from grid.nrg
  Done reading the energy grid.
WARNING assign_vdw_labels: No vdw parameters for 0  s6
WARNING assign_vdw_labels: No vdw parameters for 1  o
WARNING assign_vdw_labels: No vdw parameters for 2  o
WARNING assign_vdw_labels: No vdw parameters for 3  o
WARNING assign_vdw_labels: No vdw parameters for 4  o
Element s6 not found in MW code
Element o not found in MW code
Element o not found in MW code
Element o not found in MW code
Element o not found in MW code

----------------------------------------
Molecule: 3lck

  Elapsed time for docking:	0 seconds

  Anchors:		1
  Orientations:		500
  Conformations:		94

     Grid Score:          -23.879698
       Grid_vdw:           -4.602407
        Grid_es:          -19.277290
     Int_energy:            0.000000


1 Molecules Processed
Total elapsed time:	0 seconds
-----------------------------------------

I have a couple of questions about this output and would appreciate  
your help in answering them.

1- Why I'm getting these warnings and how to fix them? Is there  
something I've missed? I assume that the Int_energy is the internal  
energy of the ligand which, in this case, has not been recognized by  
the program, and as a result, I get zero for this energy calculation.

2- If I want to compare docking results of other molecules with the  
same ligand, is the grid score a good measure to do that? Or you  
suggest using other scores implemented by DOCK?

Thanks in advance,
Laleh








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