[Dock-fans] How can I restrain certain bonds during flexible docking?

Scott Brozell sbrozell at scripps.edu
Mon Nov 17 11:42:51 PST 2008


Hi,

On Fri, 14 Nov 2008, CHIU,YEUNG wrote:

> Please excuse me for this question. I encountered with the problem 
> that I couldn't restrain a double bond when I ran the flexible 
> docking, and the results always shows twisted double bond and even 
> isomerized ligand (E to Z), which is not reasonable.

Assuming the bond types are reasonable,
the twisting is probably the result of minimization;
have you checked the basics - visualized the binding site, etc ?

See this post for comments:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-April/000982.html

An option to suppress E/Z racemization has been discussed and is on the
low priority todo list.

> I tried to follow the DOCK 6.x user manual chapter 2.7.3 to 
> manually specified non-rotatable bond, (I selected the double bond 
> and also the atoms around it, then save mol2 with "Write current 
> selection to @SETs section to file" option checked) and the 
> Chimera did write into the mol2 file some rigid requirement. 
> However the dock program still gave me same results. Did I do it 
> in the appropiate way? I'm wondering how other people deal with 
> this problem. Will some one help me out?

Manual Specification of Non-rotatable Bonds
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#ManualSpecificationofNonrotatableBonds
Currently this functionality is not available!

Scott



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