AMBER Archive (2004)

Subject: AMBER: Re: Phosphoserine residue in AMBER

From: David A. Case (
Date: Tue Aug 03 2004 - 16:23:20 CDT

On Tue, Aug 03, 2004, glegge wrote:
> I am trying to calculate the structure of a phosphopeptide with AMBER. I
> know that AMBER has been used for phosphopeptides (Wang and Wade, 2003
> Proteins, 50, 158-169 and The Kid/Kix structure by Ishwar and Peter).
> Looking through the atom mapping files that I have here at UH I do not have
> the phosphoserine residue in the mapping files (SEP). Could you send the
> appropriate atom mapping files and any advice that you can provide on how to
> approach and use this non-standard residue when you get the chance?

It _is_ a bit of a scandal that we don't have phosphorylated amino acids
as part of the standard package. Aside from adding some different protonation
forms for the standard 20, the basic Amber library has not been expanded in
more than a decade (and is really not bigger than the one we created 20 years
ago). [I'm not counting the "glycam" extensions to carbohydrates here, but
maybe I should be....]

I'm cc-ing this message to the Amber community: If you are willing to pitch
in and help Glen (and many others out), please let us know. Or just upload
things you have done to the contributed parameters web site that Richard Bryce
maintains. (Link is at the amber web page,

In a pinch, you can use antechamber to develop libraries.

...thanks in advance...dave case

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