[Dock-fans] Distorted bond Angles

Marco marco at chimfarm.unipg.it
Fri Jun 10 05:43:02 PDT 2011

Hi all!
I'm a new dock user. Following the tutorial I've performed docking studies
on my target. I'm actually docking a small molecule with a cinnamic acid
moiety in a flexible way. Unfortunately the olefine bond in the docking
solution is distorted in an unnatural manner. To overcome this problem I can
dock in the rigid way the conformers of my small molecule, but I'd like to
know if there is a way to set manually as rigid bond some bonds of my

Any advice is very appreciated. 
Thank you.


Marco Cellanetti, 
PhD Student.
Bachelor Degree in Medicinal Chemistry and Technology of Drugs

University of Perugia
Department of Medicinal Chemistry and Drug's Technology
Via del Liceo, 1 - 06123 Perugia (Italy)
Tel ++39 075 585 5169/5114

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