How Amber calculates electrostatic energy?

From: Daniel Svozil <>
Date: Wed 27 Nov 2002 15:47:11 +0100

Dear All,

I have a few questions regarding an algorithm for calculating
electrostatic energy in Sander. I am trying to get the same results
from my own little piece of force-field code as from Sander (and,
unfortunately, without any success so far).

I use a model system of methane and benzene. I obtained
the coordinates corresponding to the energy minimum from ab-initio (CCSD(T)).
I do not use Sanders to perform any minimalization, I am interested just
in a single-point calculation on the given geometry. Here are the
options I use for Sanders calculation.

imin = 0, maxcyc= 1,
ncyc = 1, drms=10.0,
ntpr = 1,
ntb = 0, ntf=1, ntc=1,
cut = 100.0,

1) In the Sander output file there are two electrostatic contributions
listed: 1-4 EEL and EELEC. 1-4 EEL is a contribution from only 1-4
intermolecular interactions, and it is scaled down by 1/1.2 factor.
EELEC contains both intramolecular contributions (1-5 and higher) and
intermolecular contributions (each with each). EELEC is not scaled at
all. The overall electrostatic contribution is the sum of 1-4 and EELEC.

Am I correct?

2) Electrostatic contribution is calculated by the following equation:

sum [(322 * q1 * q2) / distance]

q1 and q2 are partial charges taken from leap's *.lib file (or
alternatively from the *.top file, where each charge is multiplied by
18.2223), they are given as a fraction of the electron charge. distance
is given in Angstroms, 322 is 1/(4*pi*eps_0) converted to proper units.
The energy is in kcal/mol. The sum runs over the atoms we are interested
in (e.g. all atoms with 1-4 relationship).

Is the above equation correct?
If yes, when I use this equation, will I get the same results as Sander

Could somebody shed light on the algorithm, please.

Thanks in advanced

Daniel Svozil, PhD
Institute of Organic Chemistry and Biochemistry and
Center for Complex Molecular Systems and Biomolecules 
Czech Republic
phone: +420-2-20 183 263
Received on Wed Nov 27 2002 - 06:47:11 PST
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