Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

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Lee, Woonghee

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Aug 17, 2021, 1:15:32 PM8/17/21
to Jun Yang, NMR POKY/SPARKY USER GROUP, ponderosa-...@googlegroups.com

Hi Jun,

 

I guess it is driver related issue. But you don’t need to use the pymol included in the poky suite if you have the separately installed one. You can just “cd” into the BestEvaluated folder and do the job with your pymol.

 

Best,

Woonghee

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Tuesday, August 17, 2021 at 10:22 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

 

[External Email - Use Caution]Hi Woonghee,

 

Somehow the pymol included in poky runs very slow. It can take a couple seconds for any molecule movement to take effect. If I load the same pdb in the pymol we installed on the same computer, there is absolutely no lagging. Do I need to change some settings for it to work normally?

 

Thanks

 

Jun

On Friday, August 13, 2021 at 5:55:24 PM UTC-4 Lee, Woonghee wrote:

Jun,

 

Please watch the videos that I shared. You need to do some restraint validation and do calculation iteratively.

 

Best,

Woonghee

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Friday, August 13, 2021 at 3:54 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

 

[External Email - Use Caution]I got the result from the Ponderosa server. Then what's next?   Jun

On Thursday, August 12, 2021 at 6:44:43 PM UTC-4 Lee, Woonghee wrote:

Sounds great.

Sent: Thursday, August 12, 2021 4:37:02 PM


To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

[External Email - Use Caution]

Good news! I just saw the new version (2021/03/10i) of poky available so I go ahead download and install it. And the preprocess went through without a problem!!

 

Thanks!

 

Jun

 

On Thursday, August 12, 2021 at 4:20:49 PM UTC-4 Lee, Woonghee wrote:

Hi Jun,

 

Do you have your own zoom meeting room? If so, you can just join your own room, share the screen and click recording. If you have cloud recording feature, that will be a lot easier because you can just share the link to me. By the way, I have submitted a calculation job with your inputs and been waiting for the completion. It went through without any problem on my apple silicon m1 macbook pro. I will share you the result link when done.

 

Best,

Woonghee

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

 

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Thursday, August 12, 2021 at 2:17 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

 

[External Email - Use Caution]Hi Woonghee,

 

I'd be happy to do that so you can figure out the issue. How to record my operation in zoom without setting up a meeting?

 

Bests,

 

Jun

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