AMBER Archive (2005)

Subject: Re: AMBER: Protein dynamics.

From: David A. Case (case_at_scripps.edu)
Date: Mon Jun 06 2005 - 17:37:10 CDT

On Mon, Jun 06, 2005, Laurence Lavelle wrote:

> In looking at the dynamical motion of a protein, is Amber (Cornell et al.
> (1994) force field) (Amber 99 parameters) considered a reasonably realistic
> protein force field (or, as good as or better than most) ?

Don't confuse "ff94" with "ff99" [see the Amber manual for the nomenclature];
these are similar but distinct forcefields. Both will overstabilize helical
structures but are otherwise "pretty good" (tm) for folded proteins.

>
> In looking at the dynamical motion of a protein (for example using Amber),
> what are the pros and cons to doing Molecular Dynamics vs Langevin Dynamics
> vs Monte Carlo ?

Monte Carlo is an equilibrium procedure that tells you nothing about protein
dynamics. The only method for reliably looking at dynamical processes in
proteins is molecular dynamics.

>
> By protein motion I mean a folded protein in a constant temperature
> simulation (for example with a distance dependent dielectric, no
> electrostatic cutoffs, no periodic boundaries) and comparing the protein
> dynamics at different temperatures.

With the above conditions (no solvent, distance dependent dielectric) there is
little reason to expect that either the average structure or the dynamics you
see in the simulation will be realistic. If you want to get any reasonable
account of protein dynamics, you need to be looking at MD simulations in
explicit solvent. If you want good results as a function of temperature, you
should take care that the water model you are using is known to produce good
dynamical results vs. temperature for pure water.

...dac

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