AMBER Archive (2009)

Subject: Re: [AMBER] CY3 dye parameters

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Apr 25 2009 - 01:04:22 CDT

Dear James,

> 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.

You can use R.E.D.-III.2 (standalone version) or R.E.D. Server/R.E.D.-IV
With R.E.D.-III.2 you usually are able to build only a single
molecular fragment (& only some molecular fragment types) in a single
R.E.D. execution. With R.E.D. Server, you can generate as many as
molecular fragments you need in a single R.E.D. IV execution.

See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
The two logos "R.E.D.-III.x compatible" and "R.E.D.-III.x
incompatible" are used throughout the tutorial to guide the reader.

> 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.

CY3 = http://en.wikipedia.org/wiki/Cyanine ?

A Central nucleotide fragment has a total charge of -1 in the Amber
force field topology database (FFTopDB).
A 5'-terminal nucleotide fragment has a total charge of -.xxxx
A 3'-terminal nucleotide fragment has a total charge of -.yyyy
               and -.xxxx -.yyyy = -1

You said "attached to a strand of RNA": the strategy to define a
fragment for CY3 clearly depends on where you want to connect CY3: to
the central fragment ? to the 5'-terminal or 3'-terminal fragment ? do
you use a linker between the nucleotide and CY3 ? Could explain more
what you need to build ? (a drawing would help here)

Once you have understood the strategy, you could imagine different
connections to your RNA, different linkers (if any) and different
fluorescent dyes. You can thus build your own FFTopDB for fluorescent
dyes in a single R.E.D. Server job.

When building a molecular fragment the trick is to find the connecting
group(s) (or group of atoms to be removed from the whole molecule) and
the corresponding constraint so that this(ese) constraint(s) does(do)
not "brake" the system. We are developing a small module in R.E.D.-IV
so that a user will be able to "see" the impact of the constraints
used during the fit. This new feature should be available within the
next month (See the R.E.D. Server news at the R.E.D. Server home page).

regards, Francois

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