Re: Charges in NAMD topology file

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Fri Apr 20 2007 - 09:53:08 CDT

Hi all,

Actually, the charge on a given atom is its net + or - number of
electrons that belongs to it; ie, if a carbon atom has a "charge" of
-0.50, that means it has an addition "half" of an electron associated
with it. Remember from freshamn chemistry when you completed the octet
for an oxygen atom as [::O::]-2, signify it had a -2 charge, or two
additional electrons. We generally don't think of these charges as
having units, however. , and if they are involved in any calculations
(which they are) they are accounted for in the correct way by the
software code.

Richard

Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
rwoodphd_at_yahoo.com

----- Original Message ----
From: Jawahar Neelankatan <neelankatan_j_at_yahoo.com>
To: JC Gumbart <gumbart_at_ks.uiuc.edu>
Cc: namd-l_at_ks.uiuc.edu
Sent: Friday, April 20, 2007 8:10:59 AM
Subject: Re: namd-l: Charges in NAMD topology file

Thanks for the info.

JC Gumbart <gumbart_at_ks.uiuc.edu> wrote: unit electron charge (i.e. 1 = 1.6x10^-19 coulombs)
On Apr 19, 2007, at 4:51 PM, Jawahar Neelankatan wrote:

Hi all,
In the CHARMM22 proteins/CHARMM27 lipids topology file for NAMD, what are the units of the charges listed for atoms of various residues ? Coulombs ?

-Jawahar
        

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