[Dock-fans] Docking Experiment by DOCK6.4

Trent E. Balius tbalius at aol.com
Thu Jul 28 15:05:04 PDT 2011



 



When preparing the ligand be sure to assign Sybyl atom types. 

http://www.tripos.com/data/support/mol2.pdf

See page 53.

Here is an excerpt from the table.
 
O.3 oxygen sp3 
O.2 oxygen sp2 
O.co2 oxygen in carboxylate and phosphate groups
O.spc oxygen in Single Point Charge (SPC) water model
O.t3p oxygen in Transferable Intermolecular Potential (TIP3P) water model

S.3 sulfur sp3 
S.2 sulfur sp2 
S.O sulfoxide sulfur 
S.O2 sulfone sulfur

I hope this helps,


Trent


 

-----Original Message-----
From: lsoltang <lsoltang at uwaterloo.ca>
To: Trent E. Balius <tbalius at aol.com>
Sent: Thu, Jul 28, 2011 2:35 pm
Subject: Re: [Dock-fans] Docking Experiment by DOCK6.4



Hi Trent.

Thanks for your reply.

Quoting "Trent E. Balius" <tbalius at aol.com>:

>
> 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).

Actually, I've followed the Chimera based preparation for the receptor  
and ligand, as written in the manual.


>
> 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
>
>

Yes. I had seen this before, but can't understand how to fix the  
problem. The case-sensitivity, which has been mentioned there, should  
be causing my problem, too. This is my lig_charged.mol2 file:

---------------------------------------
@<TRIPOS>MOLECULE
3lck
5 4 1 0 0
SMALL
AMBER ff99SB


@<TRIPOS>ATOM
       1 S          20.2280   32.6940   68.9680 s6         1 SO4901      1.5428
       2 O1         19.7900   31.9210   70.0890 o          1 SO4901     -0.8852
       3 O2         19.0940   33.1530   68.2330 o          1 SO4901     -0.8852
       4 O3         21.0160   33.8150   69.3880 o          1 SO4901     -0.8852
       5 O4         21.0300   31.8710   68.1250 o          1 SO4901     -0.8852
@<TRIPOS>BOND
      1    1    2 2
      2    1    3 2
      3    1    4 1
      4    1    5 1
@<TRIPOS>SUBSTRUCTURE
      1 SO4901      2 RESIDUE           4 A     SO4     0 ROOT
---------------------------------------

There's no such problem with the rec_charged.mol2 file...

-Laleh



> 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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>
>
>






 
 
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