[Dock-fans] How can I restrain certain bonds during flexible docking?
sbrozell at scripps.edu
Mon Nov 17 11:42:51 PST 2008
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:
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
Currently this functionality is not available!
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