Thanks very much!
Chiara
On Thu, 2012-09-20 at 07:38 -0400, Jason Swails wrote:
> On Thu, Sep 20, 2012 at 4:19 AM, Chiara Pallara <chiara.pallara.bsc.es>wrote:
>
> > Dear Amber users,
> > I am currently using MMPBSA.py Amber12 script to perform a per-residue
> > decomposition calculation on a protein-protein complex.
> >
> > My input is
> > ----------------------------------------------------
> > Per-residue GB decomposition
> > &general
> > startframe=4000, endframe=5000, interval=10,
> > verbose=1,
> > /
> > &gb
> > igb=5, saltcon=0.100,
> > /
> > &decomp
> > idecomp=1, print_res="1-484"
> > dec_verbose=1,
> > /
> > ---------------------------------------------------
> >
> > The output seems OK but there is something strange:
> > A Tyr-AMP (located in the interface between the two proteins) has a very
> >
>
> AMP is highly charged with a lot of atoms. It doesn't surprise me that the
> interaction energy is so large.
>
> Also keep in mind that free energies, even with GB, are not strictly
> pairwise decomposable since the dielectric boundary (for GB, this is the
> effective radius) is a non-local property calculated via the contributions
> of all atoms in the system. As a result, you should take these results
> with a grain of salt and don't put much stock in the absolute values you
> obtain (they can be helpful for qualitative comparisons, but "-64.76"
> doesn't mean much by itself).
>
> HTH,
> Jason
>
>
> > high energy value: -64.76 Kcal/mol. Is there something wrong?
> > Thanks in advance,
> > Best Regards
> > Chiara
> >
>
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Received on Fri Sep 21 2012 - 02:30:03 PDT
