[Chimera-users] Query

Eric Pettersen pett at cgl.ucsf.edu
Wed Feb 17 15:49:30 PST 2016

Chimera relies on the no-longer-supported Amber program sleap to add the ions, and that program was using an old leaprc (leaprc.ff02.r1) that in turn used an old ions file (ions03.lib) that had a very limited set of ions.  I have now switched to a newer leaprc for sleap (leaprc.ff14SB) and consequently newer ions lib (atomic_ions.lib) with many more ion types available, including Ca2+.

So, if you get the next daily build you should be able to add Ca2+ ions.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Feb 16, 2016, at 7:43 AM, manan <manan782 at gmail.com> wrote:
>  Chimera allows users to add ions to a given structure using Amber tools. This option has a predecided set of ions. Is it possible to add ions other than those mentioned in the add ions option. For example,Ca2+ is not included in the list, so is it possible to add Ca2+ ions?
> -- 
> Manan Desai
> Research Student
> Department of Biochemistry
> The Institute of Science
> 15 Madame Cama Road,
> Mumbai-400 032
> India
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