[Chimera-users] counter ions

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 12 10:03:32 PDT 2019

First check that your version of Chimera is not too old.  The current development Chimera (daily build) uses Ambertools 18, and the list in Add Ions is pretty long (something like 50 different types available).  There is an Ambertools 19 not yet used by Chimera, but I don’t know if that would make any difference to the list of ions.

If what you want still isn’t there, you may need to use a different program, or do something extremely approximate like adding the most similar ion, writing output files, and then manually editing the output files to contain what you want.  However, this requires detailed knowledge of the file formats, and  if you were going to use them for some further calculations, it is unclear whether or not the program(s) you will be using for the calculations would also be able to handle that molecular species.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 12, 2019, at 5:54 AM, patrizio.arrigo at ge.ismac.cnr.it wrote:
> Dear All
>  I would like to use counter ions   of nucleic acids not included in the default list of Chimera. I do not know how to perform this action.  The option add ions offers only a limited set of ionic species 
>  I guess that is necessary to  use amber18.  Can you give me some  suggestions 
> Dr. Patrizio Arrigo

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