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On Sat, Apr 5, 2014 at 7:39 AM, Arunima Shilpi <writetoash28.gmail.com>wrote:
> Dear Sir
>
> Presently I am doing binding free energy decomposition was performed based
> on
> MM/GBSAdelta and MM/PBSA .
>
> I want to plot energy contributions from each residue with the ligand thus
> plotting ligand-residue inteaction scpectra.
> Kindly guide me with the command to be used to study the interaction.
>
It is impossible to prepare a command (script or program) with Amber that
will do EVERY type of analysis people would want. Analyzing data that is
generated _from_ an analysis program is typically not the domain of Amber
programs. For instance, it may be a plotting program like gnuplot,
xmgrace, or some spreadsheet coupled with either a clever little script you
wrote or a bit of work copying numbers from one place to another.
To create the plots you want, you can do any number of things -- you can
copy your data into a spreadsheet (like MS Excel or
OpenOffice/LibreOffice), you can write a script to postprocess the data and
put it into a format understood by xmgrace or gnuplot, you can write a
Python script with the matplotlib library to postprocess and plot in the
same step, you can do the same in matlab, etc.
Long story short, this step is up to you.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Apr 05 2014 - 06:00:02 PDT
