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

CHIU,YEUNG adolphsdchiu at ufl.edu
Fri Nov 14 11:32:47 PST 2008

Hello everyone,

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.

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?

Thank you for your help! And sorry to bother the others.

Sincerely yours

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