On 5/31/05, masi.nmr.mpibpc.mpg.de <masi.nmr.mpibpc.mpg.de> wrote:
> Hi amber community,
>
> I want to calculate the binding free energy of a ligand to a protein. Is the following the right way to do this: First, run a MD of
> the ligand bound to the protein (i.e. the complex) and then post-process the trajectory with the mm_pbsa.pl (in amber8)
> script? Why is default "nmode=0" ? Doesn't one need to calculate the entropy with nmode to get a binding free energy at all?
That is correct. Nmode however require significant processor time, so
that a second run (solely for entropy determination) using a smaller
subset of trajectories is often favorable.
> I am a complete rookie on this subject, so any help is greatly appreciated!
>
> Best wishes,
>
> Martin
>
>
>
>
> ---------------------------------------------------------------------------------------------------------
> Martin Sippel
> Max-Planck-Institut für biophysikalische Chemie
> Abt. NMR-basierte Strukturbiologie, Office 5
> Am Fassberg 11
> D-37077 Göttingen
>
> Tel.: +49 551 201 2215
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Jun 02 2005 - 00:53:00 PDT
