Hi Eric. Maybe this will help.
Small python script that creates as output the info needed for
titration_curves.dat
Substitute MOL for the name of the residue you are titrating.
On line 7, the line.split()[3], the '3' should be changed to the number
pertinent to the column that has the deprotonated data.
This script is valid for a single residue titration.
1 from numpy import linspace
2 lst = []
3 for i in linspace(1,5,10):
4 with open('ph{:.1f}_populations.dat'.format(i)) as f:
5 for line in f:
6 if 'MOL' in line:
7 lst.append(line.split()[3])
8
9 print('#{:<5}pH{:<5}MOL1'.format(' ',' '))
10 for j,n in zip(linspace(1,5,10),lst):
11 print('{:>8.3f}{:>6}{:.3f}'.format(j,' ',float(n)))
Fabrício
2016-12-05 14:36 GMT-02:00 Eric Lang <eric.lang.bristol.ac.uk>:
> 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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Received on Mon Dec 05 2016 - 09:00:03 PST
