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
(angstrom)
the scaling factor is 18.22 which is square root of 332.
Sincerely,
Wei
Received on Sun Jan 27 2008 - 06:07:32 PST
