On Thu, 2014-02-20 at 09:09 -0600, Javier Alejandro Rendon Carrillo
wrote:
> Hi DAC!
>
> I´ve working in the MMPBSA.py method using a DNA-Protein complex, im
> following this tutorial
> http://ambermd.org/tutorials/advanced/tutorial3/section2.htm , now i have a
> question after execute the pruduction
> run.x how i get the plots of the the
> density<http://ambermd.org/tutorials/advanced/tutorial3/files/prod_summary.DENSITY>
> , temperature<http://ambermd.org/tutorials/advanced/tutorial3/files/prod_summary.TEMP>
> , total energy<http://ambermd.org/tutorials/advanced/tutorial3/files/prod_summary.ETOT>
> and
> backbone RMSD<http://ambermd.org/tutorials/advanced/tutorial3/files/measure_prod_rmsd.ptraj>
> .
> should i use the same command line used before ./process_mdout.pl heat.out
> density.out equil.out
> what is the command line need to get the plots?
Those plots are generated using xmgrace, I believe. There are no
scripts bundled with that tutorial that create those plots automatically
as far as I know.
You can use the MdoutAnalyzer.py script instead of the process_mdout.pl
script if you wish to plot the results from an mdout file quickly.
Details are in the AmberTools 13 manual, but if you just run
MdoutAnalyzer.py <mdout> [<mdout2> [<mdout3> ... ]]
it will bring up a GUI that you can point and click around to plot
various data found in the mdout. You have to have numpy and matplotlib
installed to use this script.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 20 2014 - 07:30:08 PST
