AMBER Archive (2004)

Subject: AMBER: FEP along a reaction coordinate in sander

From: Tomasz Borowski (borowski_at_physto.se)
Date: Wed Dec 01 2004 - 02:46:54 CST

Dear All,

I'd like to do FEP calculations along (ab-initio)
reaction path for a small organic system in water.
(to get the solvation contribution to the activation
free energy). Let's say I have the coordinates for
several points along this path with corresponding
RESP charges. Can I use sander to do TI along this
path? I assume I can perturb the charges and VDW
parms, but can I change the geometry when changing
lambda?

I'll be greatful for any suggestions,

best regards,

Tomasz Borowski
   

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