Docking problem in my Protein ligand
Hi hope you are fine? I cant find out the final result by protein ligand docking by chimera. This shows the error with pdb receptor. What can i do ?
Dear Muhammad, The web service that was used by the "Autodock Vina" tool in Chimera is no longer available. To use this tool in Chimera, now you have to download and install Autodock Vina on your own computer, as explained in the help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Or, you could use some other docking program or web service (not in Chimera). There are many good docking programs developed by other groups, including: Autodock Vina <http://vina.scripps.edu/> DOCK <http://dock.compbio.ucsf.edu/index.html> Web services: Swissdock <http://www.swissdock.ch/> Webina <https://durrantlab.pitt.edu/webina/> For virtual screening, DOCK Blaster: <https://blaster.docking.org/> After you do the docking separately from Chimera, you could still use the ViewDock tool in Chimera to analyze the output files. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.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 26, 2020, at 9:12 PM, MUHAMMAD FURQAN AKBER <f2018140043@umt.edu.pk> wrote:
Hi hope you are fine? I cant find out the final result by protein ligand docking by chimera. This shows the error with pdb receptor. What can i do ?
I also used downloded autodook vina in chimera On 27 Aug 2020 8:04 p.m., "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Dear Muhammad, The web service that was used by the "Autodock Vina" tool in Chimera is no longer available. To use this tool in Chimera, now you have to download and install Autodock Vina on your own computer, as explained in the help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
Or, you could use some other docking program or web service (not in Chimera). There are many good docking programs developed by other groups, including:
Autodock Vina <http://vina.scripps.edu/> DOCK <http://dock.compbio.ucsf.edu/index.html>
Web services:
Swissdock <http://www.swissdock.ch/> Webina <https://durrantlab.pitt.edu/webina/> For virtual screening, DOCK Blaster: <https://blaster.docking.org/>
After you do the docking separately from Chimera, you could still use the ViewDock tool in Chimera to analyze the output files. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/ framevd.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 26, 2020, at 9:12 PM, MUHAMMAD FURQAN AKBER < f2018140043@umt.edu.pk> wrote:
Hi hope you are fine? I cant find out the final result by protein ligand docking by chimera. This shows the error with pdb receptor. What can i do ?
It is not possible to answer your question without any information. First, make sure you change the "Executable location" in the Chimera "Autodock Vina" tool to Local and enter the location of the downloaded executable on your computer, as it says in the Help page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
That page also explains the options and what you need to do to set up the calculation. There are lots of steps and a failure might mean that you did not do them correctly, or that no docking positions are possible in the search box that you defined. If you think you did all the steps correctly but you get an error message, don't send it by e-mail here, but instead use Chimera menu Help... Report a Bug to send us the error message. In that report, you should also describe completely what steps you did before getting the error message. Or, you could try to use Autodock Vina directly (not using Chimera). See the Autodock Vina website for documentation, tutorials, etc. Elaine
On Aug 27, 2020, at 9:06 AM, MUHAMMAD FURQAN AKBER <f2018140043@umt.edu.pk> wrote:
I also used downloded autodook vina in chimera
On 27 Aug 2020 8:04 p.m., "Elaine Meng" <meng@cgl.ucsf.edu> wrote: Dear Muhammad, The web service that was used by the "Autodock Vina" tool in Chimera is no longer available. To use this tool in Chimera, now you have to download and install Autodock Vina on your own computer, as explained in the help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
Or, you could use some other docking program or web service (not in Chimera). There are many good docking programs developed by other groups, including:
Autodock Vina <http://vina.scripps.edu/> DOCK <http://dock.compbio.ucsf.edu/index.html>
Web services:
Swissdock <http://www.swissdock.ch/> Webina <https://durrantlab.pitt.edu/webina/> For virtual screening, DOCK Blaster: <https://blaster.docking.org/>
After you do the docking separately from Chimera, you could still use the ViewDock tool in Chimera to analyze the output files. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.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 26, 2020, at 9:12 PM, MUHAMMAD FURQAN AKBER <f2018140043@umt.edu.pk> wrote:
Hi hope you are fine? I cant find out the final result by protein ligand docking by chimera. This shows the error with pdb receptor. What can i do ?
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