you can read the ff99SB article to see how we developed it. it was not
based on the alanine dipeptide, but on the tetrapeptide. for the
dipeptide in the gas phase, the alpha helical conformation should not
even be a local minimum.
what is important to keep in mind is that the MP2 calculation you did
is in the gas phase- so what experiment are you using for the
comparison you mention below?
2012/1/13 Ye MEI <ymei.itcs.ecnu.edu.cn>:
> Maybe I have not made my point clear.
> AMBER force field is OK. I tried combination of 03, 99SB and IGB5, IGB1. All of them are good.
> But PESs from MP2 and FF are different. I reparametrized some ff terms according to MP2, and then I got large deviation from exp, with large population of left-handed alpha helix.
> So I guess the AMBER FF is not purely derived from MP2 calculation, but with some manual modifications. If yes, I would like to know how the developers changed the PES. Maybe I can follow them.
>
>
> Ye
> 2012-01-13
>
>
> From： Daniel Roe
> Date： 2012-01-13 21:15:47
> To： AMBER Mailing List
> CC：
> Subject： Re: [AMBER] PES for dialanine
>
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> --
> -------------------------
> 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 - 07:00:03 PST
