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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 20 2012 - 05:00:03 PDT
