Re: [AMBER] [Sender Not Verified] tleap ion naming issues

From: Steinbrecher, Thomas via AMBER <>
Date: Tue, 14 Feb 2023 08:46:54 +0100

Hi Gonzalo,

can you post the commands you use and the errors you get? This helps with

In this case, isnt the Fe3+ ion just called FE, not FE3?

in xleap, 'list' shows you the defined molecules and 'edit FE' will bring
up a panel that allows you to inspect if that is the moiety you want.

Kind Regards,


On Mon, Feb 13, 2023 at 8:41 PM Gonzalo R. Vazquez-Jimenez via AMBER <> wrote:

> Hi everyone,
> I am trying to add Fe3+ ions to my system in leap, however, I have tried
> using Fe3+ and FE3 as the names for the ion when I use the addions command.
> I know that FE2 works when I want to add Fe2+ to my system. I am sourcing
> the ff14SB force field and tip3p water model libraries, which should
> include this ion. Any help would be appreciated.
> Thanks,
> Gonzalo Vazquez
> St. John's University
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*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
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Received on Tue Feb 14 2023 - 00:00:03 PST
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