Hello Martin-- > > 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. >
Why don't we fix these parameters? What happens if you ask PRODRG to give you, say methylcyclohexane? Does minimizing this structure give undesired twist boat conformation? If not, we can use those parameters to fix those of CHEX. I'm happy to help with that. best regards-- Charles _______________________________________________ Xplor-nih mailing list Xplor-nih@cake.cit.nih.gov http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
