AMBER Archive (2006)

Subject: Re: AMBER: TI, mutation

From: Pradipta Bandyopadhyay (pradipta_at_iitg.ernet.in)
Date: Mon Aug 28 2006 - 07:46:43 CDT

In your thermodynamic cycle, energy contributions coming from bond, angle
parameters of dummy atoms will cancel out.

  Pradipta

On Mon, 28 Aug 2006 eric.henon_at_univ-reims.fr 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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