On Tue, Apr 12, 2011 at 11:05 AM, <anyiphysics.gmail.com> wrote:
> Thanks Bill. I did multiple runs of perl version and I realized that the
> perl version creates a different PB/GB surface for the first frame in each
> run. Is it because of using molsurf?
>
Molsurf is a different algorithm. If MS is 1 in your perl input file, that
means you're using molsurf.
> Another question is the perl version uses atom numbers as the input while
> python uses residues numbers. So there are differences because of this?
>
As long as you pick the same atom numbers/residue numbers in each case,
there is no difference. You can't break bonds in MM/PBSA simulations when
analyzing binding free energies, there's no advantage to using atoms over
residues (unless you define a custom residue of multiple molecules...).
Also, energy decomposition is done only for residues, not for atoms (I think
only the coordinate file creation deals with atoms for the perl script).
In any case, there is rarely any need to input anything for coordinate
extraction for the Python script.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 12 2011 - 11:30:04 PDT
