Hi Tram, I should mention that this Autodock Vina tool in Chimera does not allow very much sampling. In most research situations, you would need to do a more thorough sampling, so it may be better to use the Autodock Vina program directly (not using Chimera). Using it directly allows a wider choice of parameter values, including much more sampling. The manual page for this Chimera tool mentions these limitations: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> This has also been discussed in several posts to the chimera-users list, for example: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-August/017079.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-July/015992.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 13, 2020, at 3:30 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Tram, You'll have to change the file/folder permissions for that file and/or containing folder to give yourself "write" permission. See the "File and Folder Permissions" section of this page for an explanation: How to Set File and Folder Permissions in Windows
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 12, 2020, at 4:47 PM, Tram B. Danh <tbdanh@uci.edu> wrote:
To whom it may concern, My name is Tram Danh, a student researcher under the Radiology Department at UCI. I have encountered problems as I tried to run AutoDock Vina for a structure with At (Astatine). The system said that the atom At was not assigned or recognized.
I was told by an AutoDock member that At was not in the database so I would need to derive the parameter for At myself. I followed instructions, downloaded the default parameter file, and added At into that file. My current problem is that I am unable to save it in the "C:\Program Files\Chimera 1.14\bin\Lib\site-packages\AutoDockTools" without administrator's permission. I've attached the picture below for your reference.
Thank you for your assistance! I hope to hear from you soon!
Sincerely, Tram Danh
<ADA_parameters.PNG>