[AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Mon, 5 Dec 2016 16:36:38 +0000


I would like to calculate the pKa of the ionizable residues in my protein
after running pH-REMD simulations, using the same procedure than what is
described in tutorial 18.

In this tutorial, from the various pH_populations.dat files generated with
cphstats, the deprotonated fractions are extracted and combined in the
titration_curves.dat file prior to the fitting in gnuplot.

Could you please let me know how you created the titration_curves.dat file?
Is there a (hidden?) option in cphstats to process in an automated way the
various population files? If not, does anyone have a script that could do
that in an automated way? I just wanted to check prior to start writing

Many thanks in advance,


Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Mon Dec 05 2016 - 09:00:02 PST
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