Does it mean that using normal mode can avoid such situation? I tried to
use normal mode to calculate the entropy term but i still getting positve
binding free energy. Is it a limitation or the problem with my system
simulated?
Thank you.
On Tue, Jan 22, 2013 at 8:56 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Jan 22, 2013, colvin wrote:
> >
> > I use mmpbsa.py to calculate the free energy binding using a set of
> > 120 snapshots and the Delta total = -14.5391 (using GB, no entropy).
> >
> > Later on, i turn on entropy=1 on the same system, and the result
> > showed that: Using Quasi-Harmonic entropy approximation: Delta G
> > binding = 32.7203 (Delta S total = -47.2595).
> >
>
> You should indeed expect big changes in the binding free energy due to
> entropy
> loss of the ligand upon binding. There are tons of articles on this: try a
> Google search on "ligand entropy loss upon binding". I'm also partial to a
> paper I wrote, that explains some of the difficulties in using the
> quasiharmonic approximation for entropies:
>
> .Article{Gohlke04a,
> author = {Gohlke, H. and Case, D.A.},
> title = {{Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
> Protein-Protein Complex Ras-Raf}},
> journal = {J. Comput. Chem.},
> volume = {25},
> pages = {238-250},
> year = {2004}
> }
>
> ...dac
>
>
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Received on Wed Jun 26 2013 - 03:30:02 PDT
