AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 06 2006 - 10:54:15 CDT

On Tue, Sep 05, 2006, Ramdas Pophale wrote:
>
> 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?

Amber94 parameters have some significant, well-known problems when they are
applied to peptides, although cyclic peptides may have enough constraints
(depending on the length and sequence) to minimize some of the problems. But
you would almost certainly be better off using ff99SB or ff03. See Chap. 2 of
the Amber manual, or Adv. Prot. Chem. 66:27, 2003 for more information.

Generally, the most reliable results are found with explicit solvent, but
there are lots of papers that show that results with the Amber GB/SA model and
Amber potentials are often satisfactory. These solvent models were designed
to be used with the Amber potentials for the solute.

...hope this helps....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu