Thank you Jason for your reply.
Yes, there is a bond between the complex and ligand in my case. However, I
am not trying to break any bond. Like you said, I need to find out
the energies of a particular segment of the complex, but, could you please
explain how to do "stability" analysis using decomposition?
Thanks,
Soumya
On Mon, May 19, 2014 at 6:25 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
> On May 19, 2014, at 1:19 AM, Soumya Lipsa Rath <soumyalipsabt.gmail.com>
> wrote:
>
> > Thanks for your replies.
> >
> > When I use the topology files generated by ant-MMPBSA.py I encounter the
> > following error
> > "Error: Atom mismatch in your prmtop files! Complex natom != Receptor
> natom
> > + Ligand natom."
> > The most likely reason being the terminal residues.
>
> ante-MMPBSA.py should produce topology files which are compatible with
> MMPBSA.py regardless of exactly what you are trying to do. It does not add
> or remove termini (it will remove termini if they are in the strip_mask,
> obviously, but not otherwise). I'm not sure what your problem is, but
> likely something else.
>
> > In my case I am trying
> > to find the binding energy of a portion of the complex (which lies at
> > the center) with the remaining protein, but generally when we calculate
> the
> > binding energy of the ligand molecule it generally lies at the end of the
> > complex.
>
> Is there a bond between what is considered the "complex" and what is
> considered the "ligand" in your case? It sounds like there is.
>
> > Can I get some suggestion on how to approach this problem?
>
> If you are breaking bonds, don't use MM/PBSA analyses. They will tell you
> nothing interesting or reliable (and may even mislead you). You can
> compute some interaction energies with MMPBSA.py if you do a so-called
> "stability" analysis using decomposition, so you can get the energies of a
> particular segment of the complex. Even this must be taken with a grain of
> salt, though, as solvation effects are not strictly decomposable (as they
> are many-body effects), so certain approximations are being made.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Mon May 19 2014 - 22:00:02 PDT
