AMBER Archive (2008)

Subject: Re: AMBER: chromophore parameters for Molecular Dynamics

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jan 11 2008 - 14:57:19 CST

Quoting Anthony Cruz <acb15885_at_uprm.edu>:

> 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:
http://pps.cryst.bbk.ac.uk/PPS2/projects/jonda/chromoph.htm

If so, this is a pseudo amino-acid (AA):
For deriving a FF library for a new central fragment (AA) see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
& more particularly:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10

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
http://pubs.acs.org/cgi-bin/abstract.cgi/joceah/2007/72/i24/abs/jo071248a.html
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
protected.

regards, Francois

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu