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From: Daniel Svozil <svozil_at_uochb.cas.cz>

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

gives?

Could somebody shed light on the algorithm, please.

Thanks in advanced

Dan

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

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 263Received on Wed Nov 27 2002 - 06:47:11 PST

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