Re: [AMBER] L and D peptides

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Tue, 20 Jul 2010 13:12:08 -0700

Please excuse my lack of chemistry, but is the D-isomer
chemically different from the L? If they are chemically
the same, all you should need is to load a pdb with the
D-isomer - as long as atoms are not missing for the template
to supply from its L form, things would be ok in that simulations
could be run. In this case, the only reason for developing
an L-isomer template would be to have different atomic
charges if L is not a mirror of D, or for convenience in
placing missing atoms.


> You will have to build it first, though you can name all of the residues
> TYR. The templates loaded into leap are only for the one form.

> Good luck!
> Jason

> On Tue, Jul 20, 2010 at 12:52 PM, Jorgen Simonsen <>wrote:

> > Hi all,
> >
> > I am simulating a L-Tyr-L-Tyr-L-Tyr-L-Tyr-LTyr ect peptide and want to
> > observe if the same is true for the D-isomer. I use the sequence function
> > within ambertools to generate the peptide
> >
> > seq = sequence { TYR TYR TYR TYR TYR}
> >
> > is it possible to do the same with the D-isomer or do I have to build it
> > first? Or is it already available ?

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Received on Tue Jul 20 2010 - 13:30:03 PDT
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