[Dock-fans] Docking Experiment by DOCK6.4

Trent E. Balius tbalius at aol.com
Wed Jul 27 15:41:18 PDT 2011


Hi Laleh,

Consider using a program like Chimera (Dock prep) to prepare your molecule.  This might remove some of these issues (assign Sybyl atom types compatible with DOCK). 

I believe that you are getting the warnings because the atom types assigned in your mol2 file are not Sybyl atom types and so are not specified in the VDW definition file.


See this related dock-fans posting:

http://mailman.docking.org/pipermail/dock-fans/2009-July/002170.html


See the following sections of the manual:

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#vdwdefn 
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#TriposMOL2Format

Grid Score will give you a vary rough approximation of binding energy  (single-point calculation, neglect many terms).  

Grid Score is Highly useful for applications like virtual screening. 

You may want to consider rescoring your poses with more expensive scoring functions such as GBSA or amber score.  

See Manual:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Scoring
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GridBasedScore
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Grid
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#HawkinsGBSA
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore


I hope this helps,



Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: lsoltang <lsoltang at uwaterloo.ca>
To: Dock-fans <Dock-fans at mailman.docking.org>
Sent: Wed, Jul 27, 2011 3:39 pm
Subject: [Dock-fans] Docking Experiment by DOCK6.4




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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