On Tue, Jul 23, 2013 at 5:53 PM, Yi An <anyiphysics.gmail.com> wrote:
> Hi guys,
>
> With your help I successfully ran multiple trajectory binding energy
> calculation using MMPBSA.py. However, the binding energy from multiple
> trajectory calculation is four times bigger than the binding energy from
> single trajectory calculation. After I checked the output files, I found
> that in the multiple trajectory calculation, the complex's G gas and the
> receptor's G gas is only 1/10 of G gas in single trajectory calculation. It
> looks like almost all other energy terms are the same. So I'm really
> confused here. If anyone can answer my question I would be very grateful.
> Thanks.
>
In the single trajectory approach, the internal potential terms (i.e., the
bonded terms) cancel completely since the bound and unbound conformations
are identical -- only the nonbonded terms will differ. As a result, the
terms that cancel exactly are omitted from the calculation and their
contribution is not included in any of the terms.
The internal potential terms are the bond, angle, torsion (and
urey-bradley, CMAP, and impropers for CHARMM force fields), as well as the
1-4 electrostatic and 1-4 vdW terms. Those last two can be very large. If
you set verbose=2 in the &general section of the MMPBSA.py input file, it
will add these contributions back in.
For multiple trajectories, this cancellation does not occur, and so each
term is included by default. As a note, any internal terms that do NOT
cancel in the single trajectory approach are printed and trigger a warning
in the output file (regardless of the verbose value).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 23 2013 - 17:30:02 PDT
