AMBER Archive (2005)

Subject: Re: AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time

From: Nelson Fonseca (nfonseca_at_dq.ua.pt)
Date: Wed Nov 30 2005 - 15:33:09 CST


On Wed, 2005-11-30 at 13:15 -0500, Lihong Song wrote:

> Dear Amber user,
> I want to plot the "Ggas+Gsol" as a function of time after MM-PBSA
> calculation. Does anyone know how to extract the total energy of each
> snapshot from the MM-PBSA output?
> I appreciate your help.
>
> LSOng
>
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-- 
Nelson Fonseca <nfonseca_at_dq.ua.pt>

Hi!

Its simple. You can write a Perl, Python or Awk script using regular expressions and have the values of interest from mm-pbsa output files extracted in such a way you can plot them against the simulation time. Take a look on the "re" module of Python.

Good Luck!

Nelson Fonseca Molecular Modeling Lab. Department of Chemistry University of Aveiro PORTUGAL


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