Not, sure but it’s worth a look if you find exactly what you want in charm it has both previously calculated topology and parameters and of course you can also ask it to calculate them… not sure what it does for linkage of protein dna rna or protein like structures
Sent from Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: Charles Schwieters <[email protected]> Sent: Wednesday, June 11, 2025 8:32:36 PM To: Xplor-NIH mailing list <[email protected]> Cc: Gary Thompson <[email protected]> Subject: Re: PNA structure calculation Hi Gary-- Does the ATb contain PNAs with linkage information? I think the CHARMM files should have that directly. Charles On Wed, 11 Jun 2025 15:18:44 -0400, Gary Thompson wrote: > > [1 <text/plain; utf-8 (base64)>] > [2 <text/html; utf-8 (base64)>] > Would the ATB > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fatb.uq.edu.au%2F&data=05%7C02%7CG.S.Thompson%40kent.ac.uk%7Cbcf14723de034d6a370e08dda91ebf9f%7C51a9fa563f32449aa7213e3f49aa5e9a%7C0%7C0%7C638852671727824265%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=BHqR4IR0bcpmycQi3d23eSSyjRg4ITFoav6MsLFfAls%3D&reserved=0<https://atb.uq.edu.au/> > be of some use as well? > > regards > Gary > > Dr Gary S Thompson NMR Facility Manager > CCPN CoI & Working Group Member > Wellcome Trust Biomolecular NMR Facility > School of Biosciences, Division of Natural Sciences > University of Kent, Canterbury, Kent, England, CT2 7NZ > > ☎:01227 82 7117 > ✉️: [email protected] > orchid: orcid.org/0000-0001-9399-7636 > > On 11 Jun 2025, at 20:15, Charles Schwieters <[email protected]> > wrote: > > Hello Yoanes-- > > I am Yoanes from Ghent University. Recently, we planned to calculate > structure based on NMR data regarding DNA:PNA-small molecule > conjugate complex. Is there a certain nomenclature to build the > topology and parameter files for PNA residues? > > A good starting point might be the CHARMM PNA parameters- I am certain > that these can be adapted for use in Xplor-NIH. You might obtain these > parameters, and then contact me if you need assistance in building > Xplor-NIH .top and .par files. > > best regards-- > Charles > > ######################################################################## > > To unsubscribe from the XPLOR-NIH list, click the following link: > Bad URL Removed - see why - > > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fees.sps.nih.gov%2Fservices%2FPages%2FAnti-Virus.aspx%253FSUBED1%253DXPLOR-NIH%2526A%253D1%26data%3D05%257C02%257Cg.s.thompson%2540kent.ac.uk%257Cbda9b8872a8d43fa62e608dda91c58fd%257C51a9fa563f32449aa7213e3f49aa5e9a%257C0%257C0%257C638852661571846715%257CUnknown%257CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%253D%253D%257C0%257C%257C%257C%26sdata%3DIoNqoTP3ycKd2auPlHn9OHp45DpgVyjFy9h53jgw3oA%253D%26reserved%3D0&data=05%7C02%7CG.S.Thompson%40kent.ac.uk%7Cbcf14723de034d6a370e08dda91ebf9f%7C51a9fa563f32449aa7213e3f49aa5e9a%7C0%7C0%7C638852671727847514%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=rKrL7Q7w8b9VPfPrZYvJmv6jMj1ctFsM1qCZ398380c%3D&reserved=0<https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx%3FSUBED1%3DXPLOR-NIH%26A%3D1&data=05%7C02%7Cg.s.thompson%40kent.ac.uk%7Cbda9b8872a8d43fa62e608dda91c58fd%7C51a9fa563f32449aa7213e3f49aa5e9a%7C0%7C0%7C638852661571846715%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=IoNqoTP3ycKd2auPlHn9OHp45DpgVyjFy9h53jgw3oA%3D&reserved=0> > > > ------------------------------------------------------------------------------- > > To unsubscribe from the XPLOR-NIH list, click the following link: > Bad URL Removed - see why - > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fees.sps.nih.gov%2Fservices%2FPages%2FAnti-Virus.aspx%3FSUBED1%3DXPLOR-NIH%26A%3D1&data=05%7C02%7CG.S.Thompson%40kent.ac.uk%7Cbcf14723de034d6a370e08dda91ebf9f%7C51a9fa563f32449aa7213e3f49aa5e9a%7C0%7C0%7C638852671727865676%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=rR03Jz83BRuGZudUF3pvniiyO1r9fLJ9hQx26acq5aQ%3D&reserved=0<https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=XPLOR-NIH&A=1> ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
