Hi folks, after many years away from these types of peptides I'm revisiting NMR structure calculations of Cha containing peptides. But I'm having problems getting functioning TOP and PAR parameters for Cha. The ones supplied in the current Xplor-nih release are still giving the same errors as I was getting 10 years ago, when for some published work we had to abandon using the CHEX patch and just model them as leucine instead. Does anyone have any NMR parameters for Cha that they know work? Everything I have tried either in the past either using supplied Xplor parameters dating back to Xplor 3.5 or from other online resources (PRODRG2, XPLO2D, HICUP) either had no hydrogens or gave nasty twist boat high energy structures or structures that appear to have low energies but still have bad twist boat forms. In recent times I have also tried parameters put through the Mark groups Automated Topology Builder (ATB), but those too also give twist boats but also occasionally nice cyclohexane boats but other errors within the structure. If you'd like a visual aid for what I mean I won't post the link here, but if you search Dr Google for "The trouble with Cha" you'll find a summary of my recent frustration.
So does anyone have any parameters that work for Cha? Presumably something about having 8 contiguous sp3 carbons is mucking up the impropers. regards, Martin _____________________________________________________ Dr. Martin Stoermer Senior Research Officer INSTITUTE FOR MOLECULAR BIOSCIENCE University of Queensland 4072 AUSTRALIA Phone: +61-7-3346 2991 Fax: +61-7-3346 2101 _____________________________________________________ _______________________________________________ Xplor-nih mailing list Xplor-nih@cake.cit.nih.gov http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
