Re: amber-developers: charges in mol2 versus prmtop

From: Wei Zhang <>
Date: Fri, 25 Jan 2008 16:40:20 -0600

Carlos P. Sosa wrote:
> Hello,
> Does anybody know where the scale factor of about ~18 between charges
> printed in the mol2 file and charges printed in the prmtop file?
> Thanks

Dear Carlos,

It comes from the coulomb potential:

                                         V(r) = K * qi *qj /r

 K = 9e9 J*m/C2
while in mol2 the charge is in unit of electron which 1e = 1.602e-19 C

In amber the energy unit is Kcal/mol, 1 Kcal = 4200 J, to convert to
mol you

need avergadro's number which is 6.023e23. the unit distance is angstrom
(1e-10 m)

The overall formula will be:

            V (kcal/mol) = 332.0 qi (elector) * qj (electron) / r

the scaling factor is 18.22 which is square root of 332.


Received on Sun Jan 27 2008 - 06:07:32 PST
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