On Fri, Apr 19, 2013 at 2:07 AM, Catein Catherine <askamber23.hotmail.com>wrote:
> Dear Sir/Madam,
> In the "$AMBERHOME/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue"
> directory.
> I found the output file "test_statistics.out.save". I have a problem how
> to interpret the result.
> In this run, the complexes composes of residues 100 to 210, receptor
> composes of residues 100 to 110, the ligand composes of residues 200 to 210.
> In the output file, I found a series of energies at the delta subheading,
> which composes of residues 100-110 and 200-210.
> What is the physical meaning of these delta values?
>
It is the energy of that residue in the complex minus the energy of that
residue in the receptor or ligand. Basically, it's how the energy of that
residue changes between the bound and unbound states.
For pairwise decomposition, it's the change in the interaction energy
between the two residues when going from the bound state to the unbound
state. Note, all gas terms (eel, vdw, int) should be zero in this case if
both residues are part of the receptor or both are part of the ligand.
Since the solvation free energy is non-local (and not
pairwise-decomposable), the pol and/or sas terms may _not_ be zero (and
won't be if either/both residues are close to the binding site).
> If I sum all the delta values under the column of "TPBTOT", is it same as
> the total binding energy of receptor to the ligand?
I'm not sure here. It certainly won't be the same if you don't print out
the contributions of all residues. I'm not sure how the interactions are
added to each residue. Consider residue 1 interacting with residue 2, and
that interaction energy is 10 kcal/mol. If each residue reports having 10
kcal/mol interactions, then you are effectively double-counting this
interaction energy. If, on the other hand, each residue reports having 5
kcal/mol, then the contribution was 'divided up' between these two residues
and the total energy is simply the sum of the per-residue energies.
Based on what I recall from the code, I think the energies are actually
divided up, but don't trust me completely on that. If you use MMPBSA.py to
do decomposition analysis, then the output files will contain both the
decomposed energies as well as the total energies in separate files.
These are good questions to ask, and some self-investigation would be quite
beneficial to your understanding of these values. So I encourage you to
experiment here.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 23 2013 - 05:30:03 PDT
