Re: Incorporating some ions with specific location

From: Niklaus Johner (
Date: Tue Aug 13 2013 - 08:43:04 CDT

Of course it's possible. I suggest you start by reading the psfgen manual.

My thought is you should already have ions in your pdb/psf, except if you have a good reason not to. So you just have to change the coordinates of some ions in your pdb to place them where you want. Alternatively, you can edit your pdb to add ions by hand, and then regenerate the psf (using psfgen).


Niklaus Johner
Weill Cornell Medical College
Harel Weinstein Lab
Department of Physiology and Biophysics
1300 York Avenue, Room D-501
New York, NY 10065

On Aug 13, 2013, at 4:04 AM, Stephan Grein wrote:

> Hash: SHA1
> Dear NAMD users,
> I would like to insert some Calcium ions at specific locations (x,y,z
> coordinates) in my structure (pdb/psf). Is this possible and in
> particular how?
> All the best,
> Stephan
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