Re: Magnesium Ions Placement

From: Axel Kohlmeyer (
Date: Wed Jan 27 2010 - 19:52:40 CST

On Wed, Jan 27, 2010 at 8:18 PM, Thomas Kahn <> wrote:
> I need to take a .pdb of RNA and solvate it and then add a single Mg2+ ion at specific coordinates and generate a .psf. This can be done in any order that will accomplish all three tasks: 1) solvate, 2) add one Mg2+, 3) write psf. I need to be able to specify the coordinates of the Mg2+ ion rather than having it automatically placed at a potential minima.
> Does anybody have any suggestions for me?

the psf file does not contain any coordinate information, so you would
need only one .psf file,
unless you want to remove water molecules depending on your placement
of the mg2+ ion.


> Any help would be greatly appreciated,
> Thomas Kahn

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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