Re: AMBER: Implicit Water - Force field parameters

From: Ilyas Yildirim <>
Date: Tue, 5 Sep 2006 16:22:13 -0400 (EDT)

Dear Ramdas,

When u use implicit solvent, u dont put any explicit water molecules in
your structure. In the calculations, there are 2 main effects of implicit
solvent on the energy function: electrostatic part and nonelectrostatic
part (pp. 116 of AMBER 9 Manual).

The electrostatic part is a little bit complication; it finds the
effective Born radii of atoms at each step (configuration) and
calculations the deltaG_elec described in the manual (Eq. 6.2; pp 116).
The nonelectrostatic part is very simple; it is just
  surface area * surface parameter
(surface parameter is experimentally found for different atom types).

Adding these 2 effects in the energy function, u solve the Newtonian
Motion of equations and find the velocities and so on. Namely, there is no
TIP3P water present in the explicit solvent.


On Tue, 5 Sep 2006, Ramdas Pophale wrote:

> Hello friends,
> I am contemplating using amber94 force field for simulations of cyclic
> peptides. It is an implicit solvent simulation where solvent effects are
> taken into consideration through GB-SASA models. Since the parameter files
> mention about TIP3P water model, does it mean the parameters are not
> optimized (hence not a good choice) for the implicit solvent model? If
> that's the case, could anyone suggest an alternative within or (without)
> Amber? Thanks for your time.
> Regards,
> Ramdas Pophale.

  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Sep 06 2006 - 06:07:19 PDT
Custom Search