AMBER: TI, mutation

From: <>
Date: Mon, 28 Aug 2006 12:39:48 +0000

 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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Received on Wed Aug 30 2006 - 06:07:08 PDT
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