Re: [AMBER] how to plot a graph for enthalpy

From: <psu4.uic.edu>
Date: Sat, 14 Nov 2015 14:55:27 -0600

Hi Ayesha,

   I just share my python codes to plot graph for "enthalpy" in the
tutorial here <https://sites.google.com/site/2015pcsu/data-science/mmpbsa>.
  Feel free to modify it. Please let me know if you cannot open the link.


   HTH,
   Pin-Chih

On Sat, Nov 14, 2015 at 11:29 AM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Sat, Nov 14, 2015 at 9:43 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com
> >
> wrote:
>
> > Dear Jason M. Swails,
> >
> > I am giving here a paper link because it cannot attached with this mail
> > for bigger in size, in which author plotted graph for Enthalpy's
> > and Entropy's fluctuations and the accumulated mean values. I exactly
> > want to plot graph like that please take a look on this paper. i could
> > not under stand how can he plot it. and what i
> > have to need for plotting it. here is the link of that paper:
> >
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029230/
>
>
> ‚ÄčIt seems that what that paper calls enthalpy is really just the sum of the
> MM energy terms *including* delta G solvation. This is everything except
> for the normal mode contribution. They presumably wrote a script that
> calculated these composite terms for each frame from the components that
> the MM/PBSA script produces. Their script probably also calculated the
> cumulative average and wrote a file that could be plotted easily.
>
> Note however, as I mentioned before, that what they are calling the
> enthalpy is not really an enthalpy. It has solvent entropy included.
>
> So you would need to write a script to take the output of the -eo flag in
> MMPBSA.py and process it to get the data that they plotted. Or open it in
> a spreadsheet like Excel and do your plot there. There is no tool to
> automatically create these figures for you.
>
> Alternatively, if you are comfortable with Python, you can extract the data
> directly in a Python script using the MMPBSA.py API (which is also
> described in the manual).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>



-- 
Pin-Chih Su (Henry Su)
Ph.D.
Center for Pharmaceutical Biotechnology (MC 870)
College of Pharmacy, University of Illinois at Chicago
900 South Ashland Avenue, Room 1052
Chicago, IL 60607-7173
office      312-996-5388
fax         312-413-9303
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Received on Sat Nov 14 2015 - 13:00:03 PST
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