On Thu, Feb 23, 2012, SENTHIL KUMAR wrote:
>
> 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
This is wrong; the charges you list above are actual charges, in units of
the electron charge (i.e. not multiplied by 18.22). I'm not sure where
you got them from, but I doubt that it was the prmtop file(?).
> converted it to Coulombs by multiplying it with 1.60217646 × 10-19 C
An easy (easier?) conversion is to note that Coulomb energy in kcal/mol =
(18.22)**2 * qi*qj/r, if you measure charges in atomic units and distances
in Angstroms. But I don't want to discourage you from getting experience
using other sets of units.
...dac
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Received on Thu Feb 23 2012 - 06:30:04 PST
