AMBER Archive (2006)

Subject: Re: AMBER: mm-pbsa: distant-dependent dielectric constant

From: David A. Case (case_at_scripps.edu)
Date: Sun Apr 09 2006 - 00:23:15 CDT

On Sat, Apr 08, 2006, lhsong wrote:

> In MM-PBSA, Nmode is used for entropy calculation. Why it is necessary to
> use distant-dependent dielectric constant (4r) to minimize the structure?
> another question, can I use GB model for minimization?

The second derivatives have not been coded into nmode, so you cannot use
that mode to estimate entropies.

GB modes are available for the Amber force fields in the program NAB (see the
web site below). So, that alternative is available, but it involves learning
a new program and doing the entropy part "by hand." A paper describing this
will be published soon in J. Comput. Chem.

...regards...dac

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