AMBER Archive (2006)

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

From: a a (
Date: Thu Aug 10 2006 - 21:39:54 CDT

Dear Thomas,

Thank you very much for your help!

Best regards,


>From: Thomas Cheatham <>
>Subject: Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can
>I do next?
>Date: Thu, 10 Aug 2006 16:18:00 -0600 (Mountain Daylight Time)
> > 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
> > Can I use antechamber? Or are there any references values for the
> > 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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