On Sun, Sep 2, 2012 at 11:16 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
> I am dealing with 3 complexes of the SAME ligand and three very similar
> proteins (sequence identify over 80%, structures having backbone RMSDs to
> within 1.5 angstrom). Following single trajectory MMPBSA, the ligand EEL
> varies by some 2kcal/mol.
>
> I'm asking if this is warranted and if so on what grounds?
>
Presumably the ligand adopts different conformations in the different
systems (or at least a different distribution of conformations). I would
also imagine that a single trajectory will have a std. dev. of at least 2
kcal/mol in the EEL term for the ligand, which makes it perfectly
reasonable to expect this.
Also note that ignoring other contributions to the energy (e.g., VDW,
dihedrals, etc.) may skew your interpretation of these results. For
example, a conformational change that induces a 2 kcal/mol difference in
EEL energies may be only 0.5 kcal/mol different overall.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Sep 02 2012 - 10:00:02 PDT
