Adding a New Atom To AD4 parameter file
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 [image: ADA_parameters.PNG]
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 <https://www.online-tech-tips.com/computer-tips/set-file-folder-permissions-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> _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
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>
Just a reminder that changing the permissions, on an application's files, is considered a security risk on Windows. If you are the only user of the computer, then it would be okay. An alternate, cross-platform solution would be to copy the AutoDockTools directory to a directory you control, make the modification, and then set the CHIMERAPATH environment variable to that directory. CHIMERAPATH is just like PYTHONPATH but only for Chimera. That way, Chimera will find your version instead of it's built-in version. On Windows, setting your environment variables is tricky. See How to change environment variables on Windows 10 <https://www.architectryan.com/2018/08/31/how-to-change-environment-variables-on-windows-10/>. But create a User variable, not a System one. -- Greg On 8/13/2020 3:30 PM, Eric Pettersen 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 <https://www.online-tech-tips.com/computer-tips/set-file-folder-permissions-windows/>
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 12, 2020, at 4:47 PM, Tram B. Danh <tbdanh@uci.edu <mailto: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> _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
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participants (4)
-
Elaine Meng -
Eric Pettersen -
Greg Couch -
Tram B. Danh