AMBER Archive (2009)

Subject: Re: [AMBER] CY3 dye parameters

From: Brent Krueger (
Date: Sat Apr 25 2009 - 14:33:40 CDT


Francois has brought up several important points that you need to consider
when trying to design your residue.

I'll add that what you are doing is very similar to what is done in the
tutorial A1 that you can find on the amber site.

In this tutorial a dye is attached to DNA using a C6 type linker as is
commonly used in DNA synthesis. This should provide a good starting point
for you.


On Thu, Apr 23, 2009 at 5:42 PM, <> wrote:

> I'm having problems charge getting the parameters for a CY3 dye, I
> initially
> used antechamber, but then discovered antechamber couldn't be used if you
> were
> working with a molecule fragment.
> as the CY3 dye is going to be attached to a strand of RNA, I discovered the
> program RED is supposed to be capable of getting the parameters.
> however I'm having trouble choosing a cap for the unbonded oxygen on the
> CY3
> dye, I was thinking that a suitable cap would be a PO4 group however I'm
> not
> sure what the charge should be constrained to.
> any tips?
> -James Moore
> _______________________________________________
> AMBER mailing list

Brent P.   616 395 7629
Associate Professor................fax:       616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI     49423
AMBER mailing list