AMBER Archive (2006)

Subject: AMBER: how to take care of toluene system neutrality

From: Lwin, ThuZar (
Date: Fri Aug 04 2006 - 13:27:39 CDT

Hello everyone and Dr. Case,

     I have been following Dr. Case's tutorial on thermodynamic
integration. When I write the parameter/topology file using xleap, leap
complained like this:


ERROR: The unperturbed charge of the unit: 0.084700 is not integral.


When I tried to add up the charges on xleap edited phe-> toluene, in
deed I got the net charge of 0.0847. I am aware that this is because
the charges on toluene comes from phe. I am wondering how to fix this,
so that I get neutral charge on toluene.


Thank you very much,


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