Hi,
What solvent model are you using? In simulations I have done and have seen
for various polyalanines (at least up to decaalanine) with a reasonable
solvent model and FF99SB, the most populated secondary structure type is
PP2, which agrees with expt.
On Thursday, January 12, 2012, Ye MEI <ymei.itcs.ecnu.edu.cn> wrote:
> 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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>
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Fri Jan 13 2012 - 05:30:03 PST
