Re: [AMBER] L and D peptides

From: case <>
Date: Tue, 20 Jul 2010 21:18:32 -0400

On Tue, Jul 20, 2010, Jorgen Simonsen wrote:
> 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.

Just (I hope) to clear up some of the confusion here:

With the common Amber force fields, there are no parameters that differ
between D and L amino acids. The prmtop file you make for the sequence above
is equally good for any combination of D and L amino acids.

So, to simulate one or more D-tyrosines, you need to construct an initial
model (i.e. a coordinate file) that has the correct chirality at the
alpha-carbon(s) of interest. Amber doesn't provide any simple tools to
do that. If you want *all* D-amino acids, you could make a mirror image
of an all-L peptide (e.g. by just changing the sign of the x coordinate,
leaving y and z alone); but you wouldn't really learn anything by doing
that. If you just want some of the amino acids to be D, you might need to
construct an initial structure by hand.

In the end, it's not clear what you really want to do ("observe if the same
is true for the D-isomer": what is "the same", and what is "*the* D-isomer")?
You don't have to answer such questions here, but make sure you understand
what you are trying to figure out.

...hope this helps....dac

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Received on Tue Jul 20 2010 - 18:30:03 PDT
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