[chimera-dev] Adding a New Atom To AD4 parameter file

[Elaine Meng]

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 at 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 at 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>