Re: [AMBER] About the coordinates of input or output files

From: Thomas Cheatham III <>
Date: Fri, 24 Jun 2011 14:39:21 -0600 (Mountain Daylight Time)

> I am a postdoc in CSUN and I am now using Amber11 to calculate the
> physical properties of DNA now. I have the following question.
> How are the coordinates of each atom in DNA defined in input or output
> files, i.e., how the x, y, and z axes are defined? Thanks.

The coordinate system is Cartesian, in Angstroms, with no preferred,
favored or aligned orientation. The orientation you build your initial
system will be the initial orientation (however after molecular dynamics
the molecules will likely rotate out of the initial orientation unless
otherwise restrained or constrained; there is no code at present to
directly or easily fix a particular alignment, for example to put the
helical axis on the Z-axis however there is restraint code now to
restrain plane angles; see section 6.1.1 in the Amber11 manual).

If you want a particular orientation, you could align the DNA to the principal
axis or alternatively RMS fit the DNA to put them all in the same
orientation (relative to the molecule being fit). Both can be done with


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Received on Fri Jun 24 2011 - 14:00:03 PDT
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