AMBER Archive (2006)

Subject: Re: AMBER: Implicit Water - Force field parameters

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Sep 05 2006 - 15:22:13 CDT

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.

Best,

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      -				-
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  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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