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 Post subject: Storage problem
PostPosted: Sun Feb 28, 2010 11:30 pm 

Joined: Sun Feb 07, 2010 12:37 am
Posts: 11
Hi there,

I have purchased the $79.90 package for one month for the server. Now the thing is I have nearly 1067 molecules to dock on a protein molecule. I have already docked 417 items out of which some are still under waiting procedure and two of them are calculating since yesterday. I want to know how much time does it take for a molecule to dock on a protein. coz i see very slow progress. Also if I want to dock the rest of the molecules is there a way to do it, without deleting the molecules I have already docked; which apparently the error box tell me to do? Can the process of docking become faster by any chance. As I have just 17 more days left and nearly 550 molecules to dock.

Thank you.
Prerak Shah


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 Post subject: Re: Storage problem
PostPosted: Mon Mar 01, 2010 9:41 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 40
Dear Prerak Shah,

The time needed for docking calculations increases exponentially with the number of rotatable bonds. It also depends on the box size; and more importantly, on the number of runs (ga_run option which can be set when you start a docking calculations). With the parameters you have set, it takes two-three hours for a docking run to finish, which means for 1067 molecules it should take more than a month. I suggest that you decrease the number of runs to 50 (ga_run option) so that you can finish your calculations within your subscription time.
Regarding the storage: we offer 1 GB storage place with a one month subscription. Please write us an email to info@dockingserver.com to get a quote on more storage place.

Thanks
Eszter


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 Post subject: Re: Storage problem
PostPosted: Mon Mar 01, 2010 3:59 pm 

Joined: Sun Feb 07, 2010 12:37 am
Posts: 11
Then can you please suggest me how can I change the number of runs to 50 for all those molecule which are already running or waiting to run?


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 Post subject: Re: Storage problem
PostPosted: Mon Mar 01, 2010 5:14 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 207
Under the "My Dockings" tab you can select the dockings waiting to run by checking the checkboxes and delete those using the "Delete selected dockings" command in the "More functions" menu. Then you can restart those calculations with the new settings. Please note that you are over your disk quote right now, so you should archive and delete some of your calculations or upgrade your subscription, before you will be able to start new calculations.

Kind Regards,
Zsolt


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 Post subject: Re: Storage problem
PostPosted: Tue Mar 02, 2010 3:54 am 

Joined: Sun Feb 07, 2010 12:37 am
Posts: 11
Thank you,
I guess I got my answer.
Thanks again.


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 Post subject: Re: Storage problem
PostPosted: Wed Mar 03, 2010 6:57 am 

Joined: Sun Feb 07, 2010 12:37 am
Posts: 11
Ok now when after I deleted some of the results that I din't need and tried to dock again with the same ligand molecule it gives me this error:

Wrong attach:ligand0.pdbqt


What does this mean?
Please help


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 Post subject: Re: Storage problem
PostPosted: Wed Mar 03, 2010 7:07 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 207
Please click on the ligand name in "My ligands" menu that gives this error message, and send us that URL. We need this information to investigate the problem.

Kind Regards,
Zsolt


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 Post subject: Re: Storage problem
PostPosted: Wed Mar 03, 2010 5:20 pm 

Joined: Sun Feb 07, 2010 12:37 am
Posts: 11
The thing is I have nearly 1067 ligand molecules. Basically it is a whole database of ligand molecules that I am trying to dock on my 2zej-transferase protein. The database that I am using is NCI diversity set II. You can find that under my ligands. I have the limit of docking 100 per day. So I try to select 100 ligand molecules and dock it on 2zej-transferase protein; which I use to do earlier. But only recently after that limit reached thing happened and I deleted the non-required molecules from the results and started to dock my molecules again I am facing this problem. I cannot send you the link,coz I tried to dock 100 everytime, so even I don;t know whether its a problem with one molecule or many?! Also my 4 days have gone wasted in all these errors. First the storage problem and now this. I want those days back. I am really frustrated. It use to work before and now all of a sudden this error. I need to be done with this by now, but I am still stuck just trying to get the results. Then I have to evaluate them and study them and I don't have days for it. As the server takes so long to get me the results. I also tried reducing the runs to 50 but doesn't work. Gives the same error.

Please help.


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 Post subject: Re: Storage problem
PostPosted: Wed Mar 03, 2010 5:40 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 207
Thank you for explaing the situation. We are investigating the background of the error message, I will be back with the result. Our goal is happy customers - so you can be sure that we will extend your subscription compensating these days and you will be able to finish your current calculations.

Kind Regards,
Zsolt


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 Post subject: Re: Storage problem
PostPosted: Wed Mar 03, 2010 6:03 pm 

Joined: Sun Feb 07, 2010 12:37 am
Posts: 11
Thank you so very much. I am very thankful for this gesture of yours.


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 Post subject: Re: Storage problem
PostPosted: Wed Mar 03, 2010 9:01 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 207
I have checked your ligand directory and found several problematic ligands - I moved these to the bad_ligands directory. If there is no date and time in the Finished column, it is a strong indication that there was some unexpected problem during the setup. This unexpected error is the sign of some kind of problem in the input structure. We have started 50 docking calculation to test that everything is working fine under your account and they are running without problem. Your subscription period was extended with 7 days so you will be able to finish the calculations.

Kind Regards,
Zsolt


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 Post subject: Re: Storage problem
PostPosted: Thu Mar 04, 2010 5:25 am 

Joined: Sun Feb 07, 2010 12:37 am
Posts: 11
You guys are amazing. Thank you so very much.


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 Post subject: Re: Storage problem
PostPosted: Thu Mar 04, 2010 5:37 am 

Joined: Sun Feb 07, 2010 12:37 am
Posts: 11
But now it says I have reached the maximum storage capacity. Is there a way I can see how much storage I am using?


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 Post subject: Re: Storage problem
PostPosted: Thu Mar 04, 2010 7:38 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 207
You can see the used space in the menu that appears after clicking on your login name at the top right corner, next to the Logout button. When you delete files, the system needs several minutes to hours to delete all the corresponding files stored in the database, so you should check out this menu how the available space is growing. I recommend to delete 1 docking first, which will be a fast process and then you can calculate, how many calculations do you need to archive and delete from the server.

Kind Regards,
Zsolt


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 Post subject: Re: Storage problem
PostPosted: Fri Mar 05, 2010 1:14 am 

Joined: Sun Feb 07, 2010 12:37 am
Posts: 11
Also I wanted to open the completed docked files through swisspdb viewer software and also through arguslab. Also I wanted to re-run, re-dock and re-score those molecules that I've docked here until now, using Pearls Server. Is there an easy way through which I can do this? Coz pearls server needs the related files into .pdb format which our files are, but it is somehow not accepting those files?!! Any suggestions?!

Thanks,
prerak


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 Post subject: Re: Storage problem
PostPosted: Fri Mar 05, 2010 9:46 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 207
You can use the download button in the energy table and check the protein and docked ligand checkboxes like this: http://screencast.com/t/MzhhMjlkNDct

Swiss PDB and ArgusLab will open the resulting file without problems. I have tried the Pearls Server too, but it can not even open original pdb files from the Protein Data Bank. There is also no intruction in their web page at all. So you should contact them in this regard.

Kind Regards,
Zsolt


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 Post subject: Re: Storage problem
PostPosted: Sat Mar 06, 2010 4:01 am 

Joined: Sun Feb 07, 2010 12:37 am
Posts: 11
Never in my life have I ever seen such a helpful forum and such a helpful website customer support staff. You guys are amazing. Thank you so very much for all the help every time and that too so promptly.

I will look into the pearls server thing and contact them if the problem persists. Thanks again for trying it out from your side.

-Prerak


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 Post subject: Re: Storage problem
PostPosted: Sat Mar 06, 2010 10:00 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 207
Thanks!

Zsolt


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