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

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 14 Nov 2015 12:29:15 -0500

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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Received on Sat Nov 14 2015 - 09:30:03 PST
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