amber-developers: Implicit Solvent and dummy atoms

From: Ilyas Yildirim <>
Date: Thu, 31 Aug 2006 18:38:10 -0400 (EDT)

Dear All,

I am trying to make some changes in the AMBER code to use implicit solvent
in structures which have dummy atoms in it. The current version does not
let me do it (implicit solvent simulations see dummy atoms as real atoms
and as a result effect the solvation free energy).

Eq. 6.2 (pp. 116 of AMBER 9 manual), which is the elec. free energy of
solvation, depends on f_GB. And f_GB depends on R_i's, effective Born
Radiaas (Eq. 6.3 in pp. 117). The code is written such that R_i'a are
found using Eq. 6.6 (pp.118):

1 / R_i = 1 / rho_i * tanh(alfa*psi - beta*(psi)^2 + gamma*(psi)^3)

where rho_i's are the van der Waals radiuses (or PB radiuses),
alfa/beta/gamma are constants and psi is defined as

psi = I * rho_i,

where the integral, I, is defined in Eq. 6.5 as

I = 1/(4*phi) * integral_of_solute{ teta(|r| - rho_i) * 1/r^4 * d^3r }

If the van der Waals radius of dummy atoms are defined as equal to zero,
the system will give NaN results. I am trying to track down where this is

f_GB wont be ever zero because of r_ij part in it. And because the dummy
atom charges are equal to zero, deltaG_el wont be affected by the dummy
atoms. I am thinking that dummy atoms are effecting the Born radiaas
somehow. Born radiaas depend on both the integral and the van der Waals
radiuses. If the vdW radius of dummy atoms are defined to equal to zero,
the calculation of the Born radius of the dummy atoms will blow up because
of 1/rho_i term. Other than that, I am not sure how the integral part is

If someone can direct me to the place where the integral calculation is
done, I will appreciate it. I assume that the integral part is not
responsible of these NaN results, because the integrals are done over the
solute atoms (excluding the i_th atom), but I would like to see what kind
of approximation is done to calculate these integrals. Thanks in advance.


  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-
Received on Sun Sep 03 2006 - 06:07:16 PDT
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