AMBER Archive (2008)

Subject: Re: AMBER: amber: parameters for 5' nucleotide monophosphates

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Oct 13 2008 - 14:44:47 CDT

Quoting Jeff Schwinefus <schwinef_at_stolaf.edu>:

> I apologize if this has already been asked, but do parameters for
> isolated 5' nucleotide monophosphates (net charge = -2) exist? I have
> been unable to find any information about these nucleotides in the
> reflector archive, Amber website, and Amber manual. The closest
> structures to what I want are the DA3, DC3, ..., RA3, RC3, ...
> nucleotides in Amber, but they lack the proper phosphate structure and
> charge for isolated nucleotide monophosphates.
>
> If these isolated nucleotides monophosphates need to be designed
> similar to tutorial #A1, by chance do parameters and RESP charges exist
> for methyl phosphate (-2 charge) exist? I have searched the REDDB, but
> I have not found any information for this ion.

We have FF libraries for many coenzymes: They will be available in
R.E.DD.B. soon.

We have any types of 5'-phosphorylated-3'OH-2'OH-nucleotides such as
AMP http://en.wikipedia.org/wiki/Adenosine_monophosphate, CMP, GMP,
UMP, but also ADP, ATP
http://en.wikipedia.org/wiki/Adenosine_triphosphate, AQP, ... UDP,
UTP, UQP, U5P

In fact, we have built: XYP, X = A, C, G, U; Y = 1, 2, 3 etc...
Phosphorylation can also be incorporated @ positions 3' and/or 2'.
Charge of terminal phosphate can be -1 or -2 as the user wish.

We have 2 force field topology databases: one compatible with the
Cornell et al. FF (parm94 up to parm99) but also for the Duan et al FF
(ff03).

If you are interested in those files I can send you the corresponding
Tripos mol2 libraries in private... Just tell what you need.

regards, Francois

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