Re: [AMBER] addions

From: Christina Bergonzo <>
Date: Wed, 6 May 2020 12:17:48 -0400


You can use the same addions command to add the number of ions that make up
your salt composition and concentration (I recommend using addionsrand).
In the following example I add Cl- ions to neutralize the charge in the
first command, and then add the desired number of ions to make up the right
salt concentration in the second command (FYI this is a large system and
I'm running with 1M salt).

addionsrand mol Cl- 0
addionsrand mol Na+ 2448 Cl- 2448

You can reference the manual for additional guidance.


On Wed, May 6, 2020 at 11:55 AM Jisha B <> wrote:

> Dear all,
> I have this system where I need to add the counterions of Na+ and the salt
> of 1M NaCl according to a protocol.
> I am aware of how to add Na+ using "addions cc Na+ 0" command in tleap. But
> I have no idea how to add the salt part. How to do that? Could someone
> guide me on this? I am a beginner.
> --
> _______________________________________________
> AMBER mailing list

Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
AMBER mailing list
Received on Wed May 06 2020 - 09:30:02 PDT
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