Dear All.
I am trying to calculate the electrostatic interaction between two toms
that are involved in Hydrogen bonding. e.g N1..H3-N3 hydrogen bond between
AT base pair.
so the non-bonded interaction is between N1 & H3 as well as N1 & N3. using
the point charge calculation formula. U = (1/4xPixE)x( (QixQj / Rij) +
(QjxQk / Rjk)) where E= 8.85418782 x 10^-12 (permitivity constant)
*Step1:I*
I go the partial charges from AMBER for N1 , N3, and N3.
D=-0.3549;
H=0.3154;
A=-0.7615;
* Step2:*
Then converted them to electron charge by dividing them by 18.2223 as
mentioned in the AMBER file format web page
http://ambermd.org/formats.html#topology
converted it to Coulombs by multiplying it with 1.60217646 × 10-19 C
*Step3:*
Dist between: Acceptot-Hygrogne is 1.9 Angstroms
Dist between Aceptor-Donor is 2.9 Angstroms
Energy Total= Energy for N1-H3 + Energy for N1-N3
Appliying this to the above formula:
N1-H3 (E1)= -8.767723e-22
N1-N3 (E2)= 6.463783e-22
Total = -2.303941e-22
Since its for per atom we need to multilple with 6.023 x 10^23 for getting
the per mole value.
So on multiplying with Avagadro numbers : Total= -1.387663e+02
I am not sure if the unit is Joules .
assuming its joules. if i convert to kcal/mol then ii get -0.033166
kcal/mole .
Usuallly the HBond energy comes in the range of 1-5 Kcal/mol.
I am sure I have gone wrong some were. I saw the energy decomp modules in
MMPBSA etc. so i attempt to recreate it just for the atoms of my interest.
My aim of this whole calulation was to make students understand the maths
and logic. But I myself is stuck. Need help in this regard.
Thank you,
Bergy
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Received on Thu Feb 23 2012 - 00:00:02 PST
