Subject: Re: CCL:Small Peptide Dynamics

From: Gregory Nikiforovich <[email-masked]>
Date: Sun, 24 Sep 1995 20:29:39 -0500 (CDT)

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                                  [email-masked]
Lopata Hall, Box 1099
St.Louis, MO 63130

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