AMBER Archive (2006)

Subject: Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next?

From: Thomas Cheatham (
Date: Thu Aug 10 2006 - 17:18:00 CDT

> I got to do the analysis for a fragement of DNA, with one of the DNA base pair
> with only PO2 remained. When I load the pdb file to xleap, it said it is not
> type, it seems that I have to define some parameters for it. What can I do?
> Can I use antechamber? Or are there any references values for the needed
> parameters that I could use?

I think what you want to do is to simulate a DNA fragment that has
terminal phosphate groups. I will assume that you have worked through the
DNA tutorial prior to trying to set up your particular system as this
should provide some grasp of what is involved. If you haven't tried the
tutorial, I strongly encourage you to do this and if there are parts you
still do not understand, please let us know so that we can improve the

The generic nucleic acid force fields with AMBER for DNA are configured
for treating hydroxylated (i.e. 5'-OH and 3'-OH) nucleic acids. The 5'
residue, named DX5 where X is A,C,T,G depending on the base lacks a
phosphate and it has an overall charge of -0.3079. The 3' residue is DX3,
contains the phosphate on the 5' side and a terminal O3' hydroxyl, and has
a charge of -0.6921 (such that if you create a 2-mer of DX5-DX3 it will
have a single phosphate and have an overall charge of -1.0 as expected).
Note that the charge is not fully localized on the phosphate (i.e. if you
add in a 5'-terminal phosphate, this will alter the charges of all the
atoms in that terminal residue and either you will have to assume that
this residue has a net-charge of -1.3079 to make it balance, or alter more
residues). The internal residues, DX, have the phosphate and a net-charge
of -1.0. If you want to look at an isolated nucleotide, the DXN
nomenclature is used.

In general, most nucleic acid simulations do not include terminal
phosphate groups, the exception being co-factors like ATP, GTP, etc (see
the parameter database mentioned below). If you actually want a free 5'-
or 3'- terminal phosphate group added, a new residue (beyond the defaults)
will have to be created. To figure out how to do this, I would (a) learn
about residue creation from the tutorials, (b) search for parameters at
the AMBER parameter database (, and/or
(c) Google the AMBER WWW page and archives. The latter (c) shows some
related hits when I search for "terminal phosphate" or "5' phosphate".
One interesting hit is the antechamber reference:

(I would also search the literature, but likely you will have to create a
terminal phosphate residue or phosphorylated terminal residue (probably
better), unless someone else on the list already has done this and is
willing to share.)

Good luck.

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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