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

From: Jason Swails <>
Date: Mon, 5 Dec 2016 13:48:15 -0500

You can create them by hand or (as I did) write scripts to generate them
for you.

I'm tracking the scripts I wrote (and used for all of my studies) in GitHub

In particular, see (that has a --help flag to
provide some usage instructions).


On Mon, Dec 5, 2016 at 11:36 AM, Eric Lang <> wrote:

> Hello,
> 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
> something.
> Many thanks in advance,
> Eric
> --
> Eric Lang
> BrisSynBio Postdoctoral Research Associate Modelling
> Centre for Computational Chemistry
> School of Chemistry - University of Bristol
> Bristol BS8 1TS - United Kingdom
> _______________________________________________
> AMBER mailing list

Jason M. Swails
AMBER mailing list
Received on Mon Dec 05 2016 - 11:00:02 PST
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