AMBER Archive (2008)

Subject: Re: AMBER: chromophore parameters for Molecular Dynamics

From: FyD (
Date: Fri Jan 11 2008 - 14:57:19 CST

Quoting Anthony Cruz <>:

> I am working in a new projec and we plan to do some molecular dynamic
> experiment to an engineered GFP molecule. I have been searching for the
> parameters for the GFP chromophore without success. Can some one help me? Any
> reference or parameters??

Do you mean something like:

If so, this is a pseudo amino-acid (AA):
For deriving a FF library for a new central fragment (AA) see:
& more particularly:

It looks like there is a diazol group in that GFP chromophore. We
developed a FF with a triazol derivative (similar group). You might
look at the Scheme 3 in the following paper
The FF is fully described in the paper. The corresponding project is
also available in R.E.DD.B., but it is unfortunately not readable as

regards, Francois

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