AMBER Archive (2002)

Subject: Re: heterochirical peptides ?

From: David Case (case_at_scripps.edu)
Date: Tue Apr 30 2002 - 13:21:38 CDT

On Tue, Apr 30, 2002, Yuguang Mu wrote:

> Will I have problems when use standard AMBER force fields to
> simulate heterochirical peptide, such as ALA- (D)ALA -PHE -???

No...both D and L forms are local minima in the potentials, with fairly
large barriers to inversion. So if you start with a D amino acid, you
should stay there.

It is possible to see chirality inversions at high temperatures, so you
should be on the lookout for that, however.

...good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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