Hello,
My comments are below.
On Mon, Jul 19, 2010 at 11:25 PM, Yan Gao <yan.gao.2001.gmail.com> 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!
Jason
> of warning, and cannot be ignored. Thanks!
>
> Best,
> --
> Yan Gao
> Jacobs School of Engineering
> University of California, San Diego
> Tel: 858-952-2308
> Email: Yan.Gao.2001.gmail.com
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jul 19 2010 - 21:30:03 PDT
