[Dock-fans] How can I restrain certain bonds during flexible docking?
adolphsdchiu at ufl.edu
Fri Nov 14 11:32:47 PST 2008
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.
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