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
here: https://github.com/swails/JmsScripts
In particular, see extract_titration_data.py (that has a --help flag to
provide some usage instructions).
HTH,
Jason
On Mon, Dec 5, 2016 at 11:36 AM, Eric Lang <eric.lang.bristol.ac.uk> 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
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>
--
Jason M. Swails
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Received on Mon Dec 05 2016 - 11:00:02 PST
