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

From: FyD <>
Date: Mon, 13 Oct 2008 21:44:47 +0200

Quoting Jeff Schwinefus <>:

> 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
UMP, but also ADP, ATP, AQP, ... UDP,

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

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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Received on Wed Oct 15 2008 - 05:08:24 PDT
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