AMBER Archive (2004)

Subject: RE: AMBER: free energy perturbation

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Tue Apr 06 2004 - 11:53:39 CDT

Herbert-
 
A little googling will get you some good info in this case--try:
 
PMF with sander module site:structbio.vanderbilt.edu
 
This will lead you to some previous posts from the archive of the amber mail
reflector on this subject (always a good place to check first). Someone else
might chime in with some amber8 advice to add to what you find there.
 
Good luck!
Kristina

>===== Original Message From Herbert Georg <hcgeorg_at_if.usp.br> =====
>Hi all,
>
>I would like to perform a free energy perturbation calculation in which
>the free energy difference reffers to inclusion of a molecule into
>another. It doesn't change its atom type, element or charge but only
>moves from the inside to the outside of the host molecule. Is this
>possible to do with AMBER?? In Leap I haven't seen this possibility,
>namely the perturbation of the position of the molecule.
>
>Thanks
>Herbert
>
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****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu

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