AMBER Archive (2004)

Subject: Re: AMBER: free energy perturbation

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Tue Apr 06 2004 - 12:03:51 CDT

Thank you very much

Kristina Furse escreveu:

>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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