[Chimera-users] Docking with UCSF Chimera

Su Datt Lam sudatt.lam at gmail.com
Wed Sep 25 00:26:10 PDT 2019

Dear Chimera,

Dear Chimera,

I am trying to use your software to run molecular docking of sucrose onto a
structure. I've provided the ligand and also the receptor structure in the

I've added the charge for the ligand (using Tools->Structure editing-> Add
charge) and selected Gasteiger ad the charge method. After that, I prep the
ligand (using Tools -> Structure editing-> Dock Prep). Then, I performed
the docking thru Tools ->Surface/Binding Analysis ->AutoDock Vina.

Vina program managed to run, but with some errors. The ligand bound to the
structure is not the right structure of sucrose, but a hairball.  I suspect
there's something wrong with the Ligand prepping method in chimera that
causes the structure to go crazy. Can you help me with this problem?

Many thanks,
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