Problem with autodock vina in chimera
Hi,
I am using the option autodocking vina in chimera and I have a problem related to the docking results. I set up the docking parameters all correct and initiate the docking run. Apparently, everything goes well, I even receive a message in chimera saying that I can see the results in the directory chosen. However, when I use the option "ViewDock" I can not see the results and I get I message saying that the file .pdbt does not appear to be dock out. Also, the docking calculation goes really fast, not like before that I used to take some time. In my inspection of the .pdbqt file created in the directory from the docking calculation (using note pad) it just has the compounds and the flexible bonds, it does not have the energies of the complexes ligand-protein.
Is there any way to correct this bug?
Thank you very much.
Luana de Campos Pharmaceutical sciences PhD. student University of Nebraska Medical Center
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Hi, I tried Chimera’s Autodock Vina interface to the web service twice today after you sent this message as a bug report, I do not see this problem: it returned results to me normally.
When results are available, Viewdock starts automatically and shows the results; you would not need to start it yourself. I do not get any message about a results directory. Tested using a recent version of Chimera. If I show the Reply Log (open from Favorites menu) it says something like this when the calculation finishes:
Job 669753 exited with exit code 0.
It may be that even though the calculation finished, because of your specific structures and choices of input parameter values, there are zero results. Or, you did not wait long enough for the calculation to finish and they were not yet written to the pdbqt file even though that file existed.
However, importantly, you should be aware that this docking web service only allows very little sampling and is not suitable for most research purposes, as stated in the boxed warning on the manual page: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.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 Jan 16, 2020, at 10:00 AM, De campos, Luana J luana.decampos@unmc.edu wrote:
Hi, I am using the option autodocking vina in chimera and I have a problem related to the docking results. I set up the docking parameters all correct and initiate the docking run. Apparently, everything goes well, I even receive a message in chimera saying that I can see the results in the directory chosen. However, when I use the option "ViewDock" I can not see the results and I get I message saying that the file .pdbt does not appear to be dock out. Also, the docking calculation goes really fast, not like before that I used to take some time. In my inspection of the .pdbqt file created in the directory from the docking calculation (using note pad) it just has the compounds and the flexible bonds, it does not have the energies of the complexes ligand-protein. Is there any way to correct this bug? Thank you very much. Luana de Campos Pharmaceutical sciences PhD. student University of Nebraska Medical Center
Also, it sounds like you might have been looking at the ligand pdbqt file (which is created so that it can be used as input to the docking step), not the docking results pdbqt file. The different pdbqt files are described in the manual page under “Output file”:
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
Elaine
On Jan 17, 2020, at 3:19 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi, I tried Chimera’s Autodock Vina interface to the web service twice today after you sent this message as a bug report, I do not see this problem: it returned results to me normally.
When results are available, Viewdock starts automatically and shows the results; you would not need to start it yourself. I do not get any message about a results directory. Tested using a recent version of Chimera. If I show the Reply Log (open from Favorites menu) it says something like this when the calculation finishes:
Job 669753 exited with exit code 0.
It may be that even though the calculation finished, because of your specific structures and choices of input parameter values, there are zero results. Or, you did not wait long enough for the calculation to finish and they were not yet written to the pdbqt file even though that file existed.
However, importantly, you should be aware that this docking web service only allows very little sampling and is not suitable for most research purposes, as stated in the boxed warning on the manual page: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.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 Jan 16, 2020, at 10:00 AM, De campos, Luana J luana.decampos@unmc.edu wrote:
Hi, I am using the option autodocking vina in chimera and I have a problem related to the docking results. I set up the docking parameters all correct and initiate the docking run. Apparently, everything goes well, I even receive a message in chimera saying that I can see the results in the directory chosen. However, when I use the option "ViewDock" I can not see the results and I get I message saying that the file .pdbt does not appear to be dock out. Also, the docking calculation goes really fast, not like before that I used to take some time. In my inspection of the .pdbqt file created in the directory from the docking calculation (using note pad) it just has the compounds and the flexible bonds, it does not have the energies of the complexes ligand-protein. Is there any way to correct this bug? Thank you very much. Luana de Campos Pharmaceutical sciences PhD. student University of Nebraska Medical Center
Also recently I'm having trouble, I was using AutoDock Vina just fine last month and this week I started using it and I have to repeat the dcking procedure twice coz' the first one doesnt wok, also the docking result is all wrong, not what it used to be. Would it be a matter of Software updating?
On Fri, Jan 17, 2020 at 6:51 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Also, it sounds like you might have been looking at the ligand pdbqt file (which is created so that it can be used as input to the docking step), not the docking results pdbqt file. The different pdbqt files are described in the manual page under “Output file”:
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
Elaine
On Jan 17, 2020, at 3:19 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi, I tried Chimera’s Autodock Vina interface to the web service twice today
after you sent this message as a bug report, I do not see this problem: it returned results to me normally.
When results are available, Viewdock starts automatically and shows the
results; you would not need to start it yourself. I do not get any message about a results directory. Tested using a recent version of Chimera. If I show the Reply Log (open from Favorites menu) it says something like this when the calculation finishes:
Job 669753 exited with exit code 0.
It may be that even though the calculation finished, because of your
specific structures and choices of input parameter values, there are zero results. Or, you did not wait long enough for the calculation to finish and they were not yet written to the pdbqt file even though that file existed.
However, importantly, you should be aware that this docking web service
only allows very little sampling and is not suitable for most research purposes, as stated in the boxed warning on the manual page:
<
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html%3E
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 16, 2020, at 10:00 AM, De campos, Luana J <
luana.decampos@unmc.edu> wrote:
Hi, I am using the option autodocking vina in chimera and I have a problem
related to the docking results. I set up the docking parameters all correct and initiate the docking run. Apparently, everything goes well, I even receive a message in chimera saying that I can see the results in the directory chosen. However, when I use the option "ViewDock" I can not see the results and I get I message saying that the file .pdbt does not appear to be dock out. Also, the docking calculation goes really fast, not like before that I used to take some time. In my inspection of the .pdbqt file created in the directory from the docking calculation (using note pad) it just has the compounds and the flexible bonds, it does not have the energies of the complexes ligand-protein.
Is there any way to correct this bug? Thank you very much. Luana de Campos Pharmaceutical sciences PhD. student University of Nebraska Medical Center
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Don, The Autodock Vina program is not included with Chimera. Chimera just sends the input to an outside web service (managed by a different research group, not ours) that is running Autodock Vina, and then shows the results when they are sent back. This is all described in the manual page for Chimera’s interface to this tool: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
I am not aware of any changes relating to this interface in Chimera nor in the web service, but it is possible there was a change in the web service that we don’t know about.
Also, as mentioned below to Luana, please consider the caveat in the boxed warning in the manual page, that this web service does not allow the amount of sampling that would be needed for most research purposes. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2020, at 5:39 PM, Don Gabo gabrielsrbio@gmail.com wrote:
Also recently I'm having trouble, I was using AutoDock Vina just fine last month and this week I started using it and I have to repeat the dcking procedure twice coz' the first one doesnt wok, also the docking result is all wrong, not what it used to be. Would it be a matter of Software updating?
On Fri, Jan 17, 2020 at 6:51 PM Elaine Meng meng@cgl.ucsf.edu wrote: Also, it sounds like you might have been looking at the ligand pdbqt file (which is created so that it can be used as input to the docking step), not the docking results pdbqt file. The different pdbqt files are described in the manual page under “Output file”:
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
Elaine
On Jan 17, 2020, at 3:19 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi, I tried Chimera’s Autodock Vina interface to the web service twice today after you sent this message as a bug report, I do not see this problem: it returned results to me normally.
When results are available, Viewdock starts automatically and shows the results; you would not need to start it yourself. I do not get any message about a results directory. Tested using a recent version of Chimera. If I show the Reply Log (open from Favorites menu) it says something like this when the calculation finishes:
Job 669753 exited with exit code 0.
It may be that even though the calculation finished, because of your specific structures and choices of input parameter values, there are zero results. Or, you did not wait long enough for the calculation to finish and they were not yet written to the pdbqt file even though that file existed.
However, importantly, you should be aware that this docking web service only allows very little sampling and is not suitable for most research purposes, as stated in the boxed warning on the manual page: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.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 Jan 16, 2020, at 10:00 AM, De campos, Luana J luana.decampos@unmc.edu wrote:
Hi, I am using the option autodocking vina in chimera and I have a problem related to the docking results. I set up the docking parameters all correct and initiate the docking run. Apparently, everything goes well, I even receive a message in chimera saying that I can see the results in the directory chosen. However, when I use the option "ViewDock" I can not see the results and I get I message saying that the file .pdbt does not appear to be dock out. Also, the docking calculation goes really fast, not like before that I used to take some time. In my inspection of the .pdbqt file created in the directory from the docking calculation (using note pad) it just has the compounds and the flexible bonds, it does not have the energies of the complexes ligand-protein. Is there any way to correct this bug? Thank you very much. Luana de Campos Pharmaceutical sciences PhD. student University of Nebraska Medical Center
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
De campos, Luana J -
Don Gabo -
Elaine Meng