AMBER Archive (2006)

Subject: Re: AMBER: TI, mutation

From: Carlos Simmerling (
Date: Mon Aug 28 2006 - 07:18:56 CDT

have you worked through the Amber tutorial on using TI?
even though it's not for ligand binding you should do it
first and then see if there are things that still are unclear. wrote:

> Hello,
> I'm a new Amber's user (version 7) and
> I want to calculate free energy changes
> with sander TI
> (more precisely a _relative_ binding free energy
> using a thermodynamic cycle).
> I understood it is
> needed to create a "frcmod" file that gives the properties of
> the dummy atoms,
> when certain atoms disappear from the initial state.
> All the examples I found on the list give
> as I expected it, zero vdw parameters in this case, but
> bond and angle parameters that correspond to
> "*real*" atoms ... (non-zero mass and non-zero force constants ?!).
> This will add potential
> energy terms which have no signification for
> the desired final state ... (? )
> Any comments will be appreciated.
> Thank you in advance.
> E. Henon
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