[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
molecule.

Any advice is very appreciated. 
Thank you.

Marco 


----
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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