Re: CCL:Small Peptide Dynamics
On Sun, 24 Sep 1995, Charles Martin wrote:
> Dawei Lin writes..
> >
> > I want to do molecular dynamics calculation of small peptides(lenght 5
> > to 8). Before I set out to do the calculations, I like to listen any
of
> > your suggests or experences.
>
.......
>
> I would be most interested in reading other opinions and
> seeing other pieces of evidence, pro and/or contrary. Anyone?
>
> Chuck Martin
>
As I understood the original question, the problem is in performing
the comprehensive conformational search for peptides of small size. In my
experience, the problem is mainly not in the force field parameters, but
in calculation protocols. All of available protocols are not perfect in
finding ALL low-energy local minima for a given peptide. However, there is
some order, from better to worse: 1) build-up procedures; 2) MD; 3) Monte-
Carlo (different options); 4) random generation of conformers; 5) systematic
search. The order is based on accuracy of predictions made by calculations
plus expences (in terms of computational time). Of course, this is my
personal opinion; more in details see my review in Int. J. Pept. Prot. Res.,
(1994) 44, 513-531.
Now, too bad that the build-up procedures are not represented in any
available commercial software. I have developed this protocol and I am
using it for many years, but this is not a commercial product (at least,
yet). If anybody really needs these calcualtions to be done, please feel free
to use my e-mail address/phone number listed below.
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Gregory V. Nikiforovich Phone (314) 935-4677
Research Professor Fax (314) 935-4979
Center for Molecular Design E-mail address:
Washington University gregory -AatT-
wucmd.wustl.edu
Lopata Hall, Box 1099
St.Louis, MO 63130
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