List/DAC,
What I would have a problem with is if one can consider the AMBER force
field as having the fidelity to accurately evaluate the energy
contribution of few H-bonds in the system relative to the overall Delta E..
Such a value calculated manually would be highly idealized and would not
be amenable to force field calculations.
The H-bond shows a great deal of variations.
The total energies can vary from 1-6 kcals/mole
There are associated blue and red IR shifts
There is a covalent component [Donor (D) ----Hydrogen (H)] and an
electrostatic component [Hydrogen (H)-----Acceptor(A)]
D ------ H --------A is not always 180 deg
H bonds can be bifuricated
The distance dependencies
1/r charge-charge electrostatic
1/r^2 charge-dipole ,, ,,
1/r^3 dipole-dipole ,, ,,
1/r^4 dipole-quadrupole polarization
1/r^6 van der Waals dispersion
And there are many other things to consider in the evaluation.
JM
On 2/22/2013 11:55 PM, Ahmed Ayoub wrote:
> Dear All,
>
> I'm trying to calculate the energy of the hydrogen bonds involved in the
> binding between two proteins. I need your help with these issues:
>
> 1- Is there an automated way to do that?
>
> 2- If not, I can go on and calculate it by hand via the non-bonded term in
> the force field. That is, I can solve this equation for the three atoms
> participating in the bond (donor, hydrogen, acceptor). If this works,
> should I calculate both VdW & Electrostatic terms or the electrostatic term
> is enough?
>
> 3- Based on (2), should I only consider the three atoms mentioned above
> only, or should I also include the atom attached to the "acceptor" atom as
> a fourth one?
>
> 4- When calculating the distance (R) between the point charges, should I
> calculate it between the centres of the atoms or the surfaces of the atoms
> (i.e. taking atom radii into account)?
>
> I really appreciate your help.
>
> Ahmed Ayoub
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Sun Feb 24 2013 - 07:00:02 PST
