Re: AMBER: free energy

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Wed, 16 Jul 2008 10:10:41 -0400

Hi all,

Let's be careful here !
A free energy profile is not a well defined quantity per-se, and MMPBSA
is really useful for binding free energies.

So, Boutheina, we need much more data about what you mean.

a.


Christopher Gaughan wrote:
> If you have a trajectory you could use the mm-pbsa module in Amber. Look at
> mm-pbsa tutorial on amber tutorial website
>
> CG
>
>
> On Wed, Jul 16, 2008 at 11:54 AM, Boutheina Kerkeni <b.kerkeni.ucl.ac.uk>
> wrote:
>
>> Hi
>>
>> Does any one knows how to compute the free energy profile with Amber?
>> Thanks
>> Regards
>> Boutheina
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry
                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
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Received on Sun Jul 20 2008 - 06:07:13 PDT
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