Dear Sir,
Thanks for the timely reply.
On Thu, Feb 23, 2012 at 7:38 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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(?).
I am sorry i got these charges from converting the PDB to PQR using amber
FF using the webserver PDB2PQR.
But any way below is the line taken from the link explaining the file format
--------------------------------------------------
%FLAG CHARGE
%FORMAT(5E16.8) (CHARGE(i), i=1,NATOM)
CHARGE : the atom charges. (Divide by 18.2223 to convert to charge
in units of the electron charge)
--------------------------------------------------------------
> > 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.
>
This really helped in the calculation. Thank u once again.
> ...dac
>
>
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Received on Thu Feb 23 2012 - 20:30:02 PST
