Dear Amber community,
Recently we plot the 2D potential energy surface of di-alanine spanned by main chain torsions (phi and psi). The structures are optimized at HF/6-31G* level, and the single point energies are calcualted at MP2/aug-ccpvtz level. And It shows large difference from that of AMBER, either 03 or 99SB. I put the PES on the web, you can download them from
http://itcs.ecnu.edu.cn/ymei/03_total_PES.pdf
http://itcs.ecnu.edu.cn/ymei/99SB_total_PES.pdf
http://itcs.ecnu.edu.cn/ymei/MP2_total.pdf
The main difference is located at phi around 70 degree, and psi between -150 and 50 degree. Has Amber force field been manually optimized, especially to reduce the population of left-handed alpha helix? If I use the MP2 PES in MD simulation of triAlanine, I get large population of left-handed alpha helix, which seems to be against the experiment.
Any comments or suggestions are welcomed.
Ye MEI
2012-01-13
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Received on Thu Jan 12 2012 - 19:30:02 PST
