How can i get aco file, and i want assign contain unnatural amino acid

[Sooho Ko]

Hello, i'm assigning peptides contain unnatual amino acid, for structure calculation.

Unnatural amino acid is AIB(2-aminobutyric acid).

I finished the peak peaking, but i can't get structure file because of AIB, and i can't import sequence file on POKY structure builder.

And for use CYANA, i want get .aco file. I tried with other short sequence, but there was no .aco or aco.tbl file.

Thank you!!.

Sooho Ko.

[Sooho Ko]

" And for use CYANA, i want get .aco file. I tried with other short sequence, but there was no .aco or aco.tbl file."

add more,

I tried with 7-mer peptide and used Poky structure builder, import sequence, chemical shift, ucsf file of noesy and tocsy, and upl file. on restraint.

Calculation option were CYANA option and AUDANA/AUDASA automation each times.

I want get prot file and aco file, but there was only prot file in final folder(BestEvalutated).

Thank you!

Sooho Ko.

2025년 6월 25일 수요일 오후 4시 36분 7초 UTC+9에 Sooho Ko님이 작성:

[Lee, Woonghee]

If you don't have aco.tbl file in the BestEvaluated, TALOS-N failed probably due to too short sequence. So it is not feasible to get angle restraints this way unfortunately. 

My suggestion is to stick with simple alternate amino acid in place of AIB until you gather enough distance restraints and switch to manual operation of XPLOR-NIH. If you use CYANA, you need to implement AIB in the CYANA library by yourself while XPLOR-NIH recently introduced it so that you can get help from XPLOR-NIH mailing list hopefully.

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

Assistant Professor & Data Science and Chemistry Certificate Program Director
Department of Chemistry
University of Colorado Denver
1151 Arapahoe St. (Science Bldg.) Rm 4128A (office), Rm 4128 (dry lab), Rm 4133 (wet lab)
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
https://clas.ucdenver.edu/chemistry/data-science-and-chemistry-certificate

Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA

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Subject: [NMR POKY/SPARKY] Re: How can i get aco file, and i want assign contain unnatural amino acid

 

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[Sooho Ko]

So much thank you Lee. Finally i got structure with your advice.

Thank you!!!!

Sooho Ko

2025년 6월 25일 수요일 오후 5시 8분 29초 UTC+9에 Lee, Woonghee님이 작성: