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From: SENTHIL KUMAR <nucleic81.gmail.com>

Date: Thu, 23 Feb 2012 13:26:01 +0530

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Feb 23 2012 - 00:00:02 PST

Date: Thu, 23 Feb 2012 13:26:01 +0530

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Feb 23 2012 - 00:00:02 PST

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