Re: Set to imit does not work

[Lee, Woonghee]

Hi Thilini,

 

The violation is subject to the calculated structure of that job not the previous one. Even if you change the restraint to meet the criterion from the current structure, it does not guarantee it is the solved problem in the next structure calculated. So, you have to run multiple times with fixed restraints. Also, if you are running “automated NOE analysis” options like AUDANA/AUDASA or PONDEROSA-X, it can introduce disabled restraint from the previous run. It has to be “constraints only-X” options.  

 

Best,

Woonghee

 

--

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

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

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From: Thilini O Ukwaththage <tuk...@lsu.edu>
Date: Thursday, April 8, 2021 at 9:51 AM
To: "Lee, Woonghee" <WOONGH...@UCDENVER.EDU>
Subject: Set to imit does not work

 

Dear Dr. Lee,

 

Hope you are doing good!

I am using PONDEROSA analyzer and when I use the "set to limit" option on some distance constraints, it does not change the number of violations to zero (nothing happens) and they are reappearing in the next distance constraints after submitting with Ponderosa client. (But some distance constraints work fine with set to limit option, not all constraints have that problem) Can you let me know how to fix this problem. I am using ponderosa analyzer built on 2020/01/21.

 

Thank you

Regards

Thilini

 

 

Thilini Ukwaththage
Ph.D. Candidate
Macnaughtan Research Group
Choppin Hall  427
Department of Chemistry
Louisiana State University

Baton Rouge, LA 70803