AMBER Archive (2002)

Subject: How Amber calculates electrostatic energy?

From: Daniel Svozil (svozil_at_uochb.cas.cz)
Date: Wed Nov 27 2002 - 08:47:11 CST

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
gives?

Could somebody shed light on the algorithm, please.

Thanks in advanced
  Dan 

-- 
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