On Tue, Jul 09, 2002, Sarangan Ravichandran wrote:
>
> I am running sander in AMBER7.
> When I look at my output file,
> I see the net charge reported as 0.5.
> Actually, the net charge in my system
> is +1.0.
>
> 2 lines from output file
> -------------------------
>
> Sum of charges from parm topology file =0.49999996
> Assuming uniform neutralizing plasma
>
>
My best guess is that you have set dielc to 4.0 (?).
Amber divides the input charges by sqrt(dielc) as they are read in;
unfortunately, this is done before the message you report above is
generated. If this is what has happened, there is no problem, but the
above message is misleading. I'll get this fixed in the next release.
If this is not the answer, we will need more information.
.good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Tue Jul 09 2002 - 20:53:47 PDT
