I recently started working with the YASARA software and I'm doing molecular docking. However, even using a small protein, I get an error that says VINA was unable to run successfully. In the user manual it says not to send a ticket to YASARA support because the problem is lack of memory, however it is a simple task and I have already defined more Gb for memory usage and I still get the same result. I'm using YASARA version 23.9.29.
Thank you in advance for your help.
Cristiano Mateus :
Just now, in response to your question, I ran a small screening docking using YASARA-Structure 23.9.29 for Windows with the new incorporated version of AutoDock Vina. The log file indicated that the docking had failed, possibly because the simulation cell was too small for the ligands. However, this was a repeat of the same docking I had done with a previous version of YASARA-Structure (that also had a previous version of Vina). Given this result along with yours, I think each of us should indeed file a report. I suspect that this is a bug that probably stems from using a new version of Vina within YASARA.
Are you using Windows, Mac, or Linux? I know that Dr. Krieger develops YASARA on Linux and then ports it to Mac and Windows. I often use Linux, and before I send my report, I will try the same docking on Linux.
Best regards and good luck,
Rudy J. Richardson
Cristiano Mateus :
I ran the same docking in the Linux version of YASARA-Structure 23.9.29, and this time it ran as expected. Moreover, it reproduced the rank order of ligand affinities as I obtained with a previous version of YASARA (and Vina). So, in my case at least, the problem seems to be with the Windows version.
When you increased the memory allocation in YASARA, what number did you use? I ask because the setting needs to be in Mb not Gb. So, for example, if you want to allocate 2Gb of RAM, this would be 2048 Mb.
Best wishes,
RJR
Dear Dr. Rudy J Richardson
First of all, I would like to thank you for your kindness in answering my question.
Regarding the problem, the operating system I used was Windows. I think that, as you suggested, the problem is a bug in the Windows version. I haven't tried running YASARA-Structure on Linux yet, but it will probably solve this problem. However, yesterday I sent the error report to the YASARA-Structure troubleshooting support team and am waiting for a response.
Regarding the memory sugestion, I don't think it will be a problem associated with this, because in addition to the protein being very small (certainly the program will have no problem performing this docking), I increased the memory by 2 Gb up to 16 Gb, taking care to always put the value in Mb.
Once again, thanks for the help and I will test it on the Linux Operating System to see if it works. However, if you could, I would appreciate it if you could send the report regarding Windows, so that the YASARA-Structure team can try to fix the problem for this Operating System.
Best Regards,
Cristiano Mateus
Cristiano Mateus :
I have already sent a report to YASARA support regarding the problem with Vina docking. I will also run some tests in Windows and Linux to see whether or not classic Autodock is affected.
Regarding RAM allocations, I usually set this at 2048 MB. Only rarely have I needed to increase the allocation above this. How were you able to allocate 16,384 MB? I thought the maximum was 10,000 MB.
Best wishes,
Rudy
Dear Dr. Rudy J Richardson
First of all, thank you very much for reporting the error to the YASARA-Structure team. Regarding the classic Autodock, I tried using it, modifying, in the code, the VINA default method by the Autodock. I think it worked on Windows without any problems. However, I've only tested the dock_run.mcr macro and did not tested with the others.
Regarding RAM allocations, I have been using the default 1500. I made a mistake when indicating the 16 Gb of memory used, I actually only used 8 Gb of YASARA-Structure memory allocation. This 16 Gb value was the memory that was being used by the computer for all tasks running. I apologize for the mistake, I actually checked now and the maximum value allowed by YASARA-Structure is in fact 10,000 Mb as you said.
Best Regards,
Cristiano Mateus
Cristiano Mateus :
I received a reply from YASARA. Apparently the issues with docking using classic AutoDock LGA and AutoDock Vina have been addressed. I downloaded the Windows and Linux versions and tested them using the dockscreening macro using both classic AutoDock LGA and AutoDock Vina. Everything now seems to be functioning as expected. Note that although the software has been repaired, the version number has remained the same (23.9.29).
RJR
Dear Dr. Rudy J Richardson
I also received an email saying that the problems had already been resolved. I haven't tested it again with the update that was made, but I believe the error has already been fixed. Yes, the version is still the same. Once again, I am very grateful for your willingness to help with this matter.
Best Regards,
Cristiano Mateus
Cristiano Mateus :
You are very welcome. I am glad that I could be of assistance. I also thank you, because your question prompted me to test the docking features in the latest version of YASARA, whereupon I found problems and got them solved by tech support.
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