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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Received on Sat Feb 23 2013 - 00:00:02 PST
