[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
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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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