Quoting "Thomas E. Cheatham, III" <cheatham.chpc.utah.edu>:
> > I am relatively new to Amber, but have not found any information on the
> > following topic. Is there an easy way to implement the D amino acids in
> > Amber? I am looking to simulate a short peptide which contains one or more
> > D-enantiomers along the backbone.
>
> As enantiomers have equivalent properties (outside of a chiral environment
> other than bending plane polarized light), one would not expect that the
> charges or intra-molecular parameters would be different for D vs. L in an
> empirical force field.
And what about introducing a D amino-acid (AA) in a sequence composed of L AA ?
Each AA (D or L enantiomer), individually I mean, is optically equivalent, but a
di-AA D-L compared to L-L are diastereoisomers. In this case, (compared to the
"ALL" L sequence), I guess, you can expect charge differences (consequently FF
param. differences).
Since the charges are derived for each "UNIT" individually (L enantiomers), the
problem could arise from mixing them which can lead to diateroeisomers. Am I
wrong or is it simply "too much" for an empirical force field ?
Regards, Francois
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Received on Wed Sep 21 2005 - 08:53:00 PDT
