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prody / ProDy

A Python Package for Protein Dynamics Analysis
http://prody.csb.pitt.edu
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No grids generated #457

Closed aminsagar closed 5 years ago

aminsagar commented 6 years ago

Dear All, I am trying to generate grids after a drugui simulation. The program exits with a success message but no dx files are generated. I am using the 5 membered rings as probes. I don't have any of the default probes. Can someone please help me with this? I would be really grateful. Regards, Amin.

jamesmkrieger commented 6 years ago

Hi Amin,

Could you tell us something more about your probes please. Did you get them from CGenFF?

Best wishes James

jamesmkrieger commented 6 years ago

Currently, DruGUI supports simulations with custom probes but not analysis unless you rename those probes to one of the default ones. If you rename them to one of these 5 e.g. IPRO then it should work to generate grids for them.

jamesmkrieger commented 5 years ago

We will develop this further at some point. Right now, we are using current scripts, which Jiyoung or Hongchun could maybe share with you or advise you on. I have assigned both of them to this issue as they are the main people working with DruGUI.

aminsagar commented 5 years ago

Thanks a lot for the help. I had this problem quite a while ago and I was able to solve it. I don’t remember for sure, but it was very likely solved by following your suggestion of renaming. May I mention that using drugui, I got the same binding sites that were discovered using a high throughput crystallisation based screening. And that too with just one day of computational time.

Thanks again for the help.

Best Regards, Amin.

On Sun, 17 Feb 2019 at 7:56 AM, James Krieger notifications@github.com wrote:

We will develop this further at some point. Right now, we are using current scripts, which Jiyoung or Hongchun could maybe share with you or advise you on. I have assigned both of them to this issue as they are the main people working with DruGUI.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/prody/ProDy/issues/457#issuecomment-464423261, or mute the thread https://github.com/notifications/unsubscribe-auth/AgXVElMK-16Gcjre_HaavL408BkB9ulcks5vOP0IgaJpZM4Qo_DP .

jamesmkrieger commented 5 years ago

Wow, that's great. Thanks for the positive feedback!