Re: [AMBER] how to neutralized my system with Na+ ions

From: Jason Swails <>
Date: Tue, 25 Aug 2015 13:12:34 -0400

On Tue, Aug 25, 2015 at 12:25 PM, Martina Devi <>

> May I know how to constrain the charge using charge derivation,as I have
> been suggested to constrain the charge to -0.3081. Should I follow the
> tutorial for charge derivation for non-standard residue?

​You can follow this tutorial:
-- just pay attention to the "prepgen" step and make sure you set the
target charge to your desired value (instead of 0).

Alternatively, RED allows you to set charge constraints like this.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Aug 25 2015 - 10:30:05 PDT
Custom Search