Re: [Chimera-users] question about AutodockVina /CHIMERA
Hi Osvaldo, Without more information, I have no idea, sorry. If you are sure that the process finished (click the “i” icon near the bottom right corner of the Chimera window to make sure), I can only say to check in the Reply Log (open from Chimera Favorites menu) and see if it says anything else useful. The Autodock Vina process does not run on our system, so there is nothing I can check here; Chimera just has an interface to send and receive results from a web service that is run by another lab, as explained in the help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> For the future, please send Chimera questions to the chimera-users@cgl.ucsf.edu address (CC’d here) to ensure they come to our attention. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2018, at 4:04 PM, ogs <ogs@ibt.unam.mx> wrote:
to whom it may concern,
hi! I am having some problems using AUTODOCK-VINA / CHIMERA.
I recently docked a linand, but I did not get the name.pdbqt file as result (I only got the name.receptor.pdb and pdbqt and the name.ligand.pdb and pdbqt)
The software show a message telling me that the process has ended and I need to check the files (but I did not see the name.pdbqt file)
What is happening? What could I do to solve this problem? Thanks a lot. Osvaldo Gómez Secundino
A few more points: If there is docking output, it would appear automatically in Chimera. That is, you would see docked structure(s) in the 3D graphics window, and a ViewDock dialog listing these results and their scores. I guess you didn’t get that either. Some things to check are that your receptor and ligand pdbqt files seem reasonable (do they contain the expected atoms?) and that the search box is a reasonable size and location. If the search box is completely filled with receptor atoms, there might not be any space to put the ligand, for example. These are all just guesses of possible things that could go wrong. I don’t know if they apply to you or not. Best, Elaine
On Jan 19, 2018, at 4:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Osvaldo, Without more information, I have no idea, sorry. If you are sure that the process finished (click the “i” icon near the bottom right corner of the Chimera window to make sure), I can only say to check in the Reply Log (open from Chimera Favorites menu) and see if it says anything else useful. The Autodock Vina process does not run on our system, so there is nothing I can check here; Chimera just has an interface to send and receive results from a web service that is run by another lab, as explained in the help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
For the future, please send Chimera questions to the chimera-users@cgl.ucsf.edu address (CC’d here) to ensure they come to our attention. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2018, at 4:04 PM, ogs <ogs@ibt.unam.mx> wrote:
to whom it may concern,
hi! I am having some problems using AUTODOCK-VINA / CHIMERA.
I recently docked a linand, but I did not get the name.pdbqt file as result (I only got the name.receptor.pdb and pdbqt and the name.ligand.pdb and pdbqt)
The software show a message telling me that the process has ended and I need to check the files (but I did not see the name.pdbqt file)
What is happening? What could I do to solve this problem? Thanks a lot. Osvaldo Gómez Secundino
Thank you so much for your answer. I tried to repeat docking I did before (when I got output) and I did not see the output this time. I only get: receptor.pdbqt and ligand.pdbqt as output. I did not get the name.pdbqt file. The software did not show any warm message or something like that. THANKS Osvaldo Gómez On Fri, 19 Jan 2018 18:31:07 -0800, Elaine Meng <meng@cgl.ucsf.edu> wrote:
A few more points:
If there is docking output, it would appear automatically in Chimera. That is, you would see docked structure(s) in the 3D graphics window, and a ViewDock dialog listing these results and their scores. I guess you didn’t get that either. Some things to check are that your receptor and ligand pdbqt files seem reasonable (do they contain the expected atoms?) and that the search box is a reasonable size and location. If the search box is completely filled with receptor atoms, there might not be any space to put the ligand, for example.
These are all just guesses of possible things that could go wrong. I don’t know if they apply to you or not. Best, Elaine
On Jan 19, 2018, at 4:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Osvaldo, Without more information, I have no idea, sorry. If you are sure that the process finished (click the “i” icon near the bottom right corner of the Chimera window to make sure), I can only say to check in the Reply Log (open from Chimera Favorites menu) and see if it says anything else useful. The Autodock Vina process does not run on our system, so there is nothing I can check here; Chimera just has an interface to send and receive results from a web service that is run by another lab, as explained in the help page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
For the future, please send Chimera questions to the chimera-users@cgl.ucsf.edu address (CC’d here) to ensure they come to our attention. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2018, at 4:04 PM, ogs <ogs@ibt.unam.mx> wrote:
to whom it may concern,
hi! I am having some problems using AUTODOCK-VINA / CHIMERA.
I recently docked a linand, but I did not get the name.pdbqt file as result (I only got the name.receptor.pdb and pdbqt and the name.ligand.pdb and pdbqt)
The software show a message telling me that the process has ended and I need to check the files (but I did not see the name.pdbqt file)
What is happening? What could I do to solve this problem? Thanks a lot. Osvaldo Gómez Secundino
Hi Osvaldo, First, make sure what you enter as “Output file” in the AutoDock Vina dialog is a location you can find and have permission to write files. Second, make sure the job is really finished (click blue “i” icon near bottom right corner of Chimera). The receptor and ligand pdbqt files are made very quickly at the beginning of the job. They do not mean that the whole job is finished. Third, see if any results are automatically shown in the Chimera 3D window and ViewDock dialog. If you can see the results in Chimera, there is an output file somewhere. It is possible the output file is just named “name” without the pdbqt part. For example, in my test I entered “~/Desktop/junk” and the results file I got was on my Desktop and named “junk”. If no output, I already gave all my ideas in the previous message. Elaine On Jan 22, 2018, at 12:25 PM, ogs <ogs@ibt.unam.mx> wrote:
Thank you so much for your answer.
I tried to repeat docking I did before (when I got output) and I did not see the output this time. I only get: receptor.pdbqt and ligand.pdbqt as output. I did not get the name.pdbqt file. The software did not show any warm message or something like that.
THANKS Osvaldo Gómez
On Fri, 19 Jan 2018 18:31:07 -0800, Elaine Meng <meng@cgl.ucsf.edu> wrote:
A few more points:
If there is docking output, it would appear automatically in Chimera. That is, you would see docked structure(s) in the 3D graphics window, and a ViewDock dialog listing these results and their scores. I guess you didn’t get that either. Some things to check are that your receptor and ligand pdbqt files seem reasonable (do they contain the expected atoms?) and that the search box is a reasonable size and location. If the search box is completely filled with receptor atoms, there might not be any space to put the ligand, for example.
These are all just guesses of possible things that could go wrong. I don’t know if they apply to you or not. Best, Elaine
On Jan 19, 2018, at 4:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Osvaldo, Without more information, I have no idea, sorry. If you are sure that the process finished (click the “i” icon near the bottom right corner of the Chimera window to make sure), I can only say to check in the Reply Log (open from Chimera Favorites menu) and see if it says anything else useful. The Autodock Vina process does not run on our system, so there is nothing I can check here; Chimera just has an interface to send and receive results from a web service that is run by another lab, as explained in the help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
For the future, please send Chimera questions to the chimera-users@cgl.ucsf.edu address (CC’d here) to ensure they come to our attention. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2018, at 4:04 PM, ogs <ogs@ibt.unam.mx> wrote:
to whom it may concern,
hi! I am having some problems using AUTODOCK-VINA / CHIMERA.
I recently docked a linand, but I did not get the name.pdbqt file as result (I only got the name.receptor.pdb and pdbqt and the name.ligand.pdb and pdbqt)
The software show a message telling me that the process has ended and I need to check the files (but I did not see the name.pdbqt file)
What is happening? What could I do to solve this problem? Thanks a lot. Osvaldo Gómez Secundino
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