[Chimera-users] Autodock vine problem

Elaine Meng meng at cgl.ucsf.edu
Sat Apr 4 07:46:59 PDT 2015

Hello Robin,
We have not seen this problem, so we would not know the reason.  You could try using Help… Report a Bug in the Chimera menu, being sure to include a description of this problem and attaching a file that includes both your input and output (for example, a Chimera session), and including your email address if you wanted a response.  However, please note that the Autodock Vina calculation is done by a web service outside of Chimera, so it might not be anything that we can fix in Chimera.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 3, 2015, at 10:04 PM, Robin <robinim30 at gmail.com> wrote:

> Hello, 
> In this context I want to that why the result of docking gives mangled ligand?
> I used web service mentioned in the last paragraph of Elaine's reply to Tunc.
> The poses listed in viewdock when observed in chimera main display, I found the ligand was not in its original structure.
> improper Bonds in ligand were added and its structure was mangled!
> What is the reason for this?
>  -Robin Parmar
> PhD Research Scholar
> Dept of Zoology,
> Gujarat University
> India.

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