AMBER Archive (2008)

Subject: Re: AMBER: free energy

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Wed Jul 16 2008 - 09:10:41 CDT


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_at_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_at_qtp.ufl.edu ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo_at_scripps.edu