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 Post subject: Make table results-error. What is the solution?
PostPosted: Tue Nov 01, 2016 2:25 am 

Joined: Wed Oct 19, 2016 4:09 pm
Posts: 2
Hello there,

Yesterday I bought a month of service and want to make good these days to perform the calculations that I should do for my research but this error occurs several molecules that interests me analyze. Then, what should i do? This problem happens me frequently with the lately docking that i did. I would like to know if this happend, there is not a manner of resolve the problem "Make results tables-error"? Or just i should take the result error like a "some irreal contacts made table preparations impossible"?

I would appreciate your early reply


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 Post subject: Re: Make table results-error. What is the solution?
PostPosted: Sat Nov 05, 2016 6:12 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 197
Firsz, try the restart button on make_result_tables process. If it does not help, it is an indication that the simulation box was not properly selected and there are clashes betweent the ligand and protein atoms. If this is the case, prepare your protein again with a modified simulation box.


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 Post subject: Re: Make table results-error. What is the solution?
PostPosted: Thu Jan 12, 2017 9:43 pm 

Joined: Fri Jan 15, 2016 10:37 am
Posts: 4
Hi there!

I get the exact same error message and when I restart the process of making the tables it does finish but much of the data is missing. I have already done runs with the same ligand and protein, and have not changed any of the parameters or the simulation box, and have not got this error message. The only thing I´m doing differently is that I´m simply doing the maximum runs of 255 now instead of 100. This is extremely annoying as I get the list of energies but when I want to study the geometry of the complex, the ligand is nowhere to be seen. I did not have this problem until very recently and now that I´ve paid for a full month, and need these simulations for my thesis, I would really appreciate if this could be fixed sooner rather than later.

Thanks!


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 Post subject: Re: Make table results-error. What is the solution?
PostPosted: Thu Jan 19, 2017 5:19 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 197
Hi,

if you send me the link I will check it for errors.

Best,
Zsolt


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 Post subject: Re: Make table results-error. What is the solution?
PostPosted: Fri Jan 20, 2017 1:58 pm 

Joined: Fri Jan 15, 2016 10:37 am
Posts: 4
Hi,

This happens for almost all of my simulations now but a link to an example is here:

http://www.dockingserver.com/web/docking/353967/?

As you can see, I cannot visualise the geometry, or get the table of interactions or the 2D figure.

Thanks,

Helgi


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 Post subject: Re: Make table results-error. What is the solution?
PostPosted: Mon Jan 23, 2017 8:39 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 197
Hi, I've checked the issue and it is basically what you suggested - 255 runs is too much to be able to process all necessary computation within a given time in your system. We have to balance between usability and security - and longer processing time is very bad for security. Now we have doubled the allowed time, so if you restart the make result table process, you have a better chance to get complete results. Besides, using 100 runs is somewhat a gold standard of docking, if you are looking to improve the accuracy of the calculation, I would rather suggest to increase the ga_num_evals to 5M or 10M instead of increasing the number of runs.


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 Post subject: Re: Make table results-error. What is the solution?
PostPosted: Mon Jan 23, 2017 9:45 pm 

Joined: Fri Jan 15, 2016 10:37 am
Posts: 4
Thank you so much for the help!

I have been evaluating the results and if I do repeated runs with 100 each time the results are just as consistent as when I do 255 for each so I will do this in the future, and will also try your suggestion of increasing the ga_num_evals to see how that will affect the accuracy!

Best regards,

Helgi


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