Re: [AMBER] problem with the total charge

From: Jason Swails <>
Date: Tue, 20 Jul 2010 00:27:08 -0400


My comments are below.

On Mon, Jul 19, 2010 at 11:25 PM, Yan Gao <> wrote:

> Dear Amber users:
> I am building a system containing ~3000 atoms and -40 charges.
> I assigned the partial charges to each atoms, and the output file says the
> total charge is -40.

What output file? Is this a number somewhere that says "total charge -40"
or something like that? Is this the mol2 file?

> However when I load the mol2 file into tleap, it told me the total charge
> is
> -39.964.

This is the sum of every partial atomic charge. Did you add up each partial
charge for each atom? What does it come out to be?

> Can any one tell me if the small charge difference is due to the system
> error during the addition of every atom? or something else?
> And how to eliminate such difference in charge? It produces an error
> instead

You should double-check your partial charges to make sure that they really
do add up to -40.000 like you think it would. This is most likely the
source of your error.

Good luck!

> of warning, and cannot be ignored. Thanks!
> Best,
> --
> Yan Gao
> Jacobs School of Engineering
> University of California, San Diego
> Tel: 858-952-2308
> Email:
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Jul 19 2010 - 21:30:03 PDT
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