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 - 06:00:06 PDT
