On Wed, Mar 30, 2016 at 6:21 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
wrote:
> Hi all,
> I want a python based code for the calculation of binding energies. i
> don’t want to use terminal command for the calculation of MMGBSA/MMPBSA. as
> used in amber advanced tutorial.
>
MMPBSA.py *is* a Python-based code for calculating binding energies.
Also note that it's not at all clear what you are asking for. There are
many ways of calculating binding energies. Alchemical transformations (TI,
FEP), end-state analyses (MM/PBSA and LIE), colvar PMF calculations
(umbrella sampling and steered MD). Nor is it clear what you mean by a
"python-based code of binding energies".
MMPBSA.py is written in Python, but is executed from the command-line. Do
you want something that is executed from the Python interpreter? If so,
why? How is that any different than just running it on the command-line?
If all you want is to have the raw data available directly in Python, then
MMPBSA.py provides an API that lets you do that *after* running the
calculation on the command-line.
What you asked for is so vague that I can't even guess how you would want
it to behave. Please try asking specific, detailed questions (
http://www.catb.org/esr/faqs/smart-questions.html). If, at the end of the
day, the existing tools (MMPBSA.py in this case) does not fill your needs,
you can always write your own.
HTH,
Jason
--
Jason M. Swails
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Received on Wed Mar 30 2016 - 06:00:05 PDT
