Re: Problem with titration curve with cphanalyze script CYS and LYS (Constant pH Molecular Dynamics )

From: Brian Radak (
Date: Fri Dec 10 2021 - 12:28:39 CST

Hi Ingrid,

This error is new to me - I'm guessing it has to do with the new dict
behavior in python 3 - - could you check which subversion you are using by
typing "python - - version"? I did not test anything after 3.7

If you could also send me the files that raise error offline, I can
hopefully have a chance to track this down.


On Thu, Dec 9, 2021, 8:02 AM Ingrid Bernardes Santana Martins <> wrote:

> Dear all,
> I have some Constant pH Molecular Dynamics to analyze. I tried to use the
> available cphanalyze script by Radak (;!!DZ3fjg!up-iYBFXcnnspe3bKDuy9mlqNBUN1xBjevNbUz0to4X1AG4hIWnUj1LU1F7cp8sKjA$
> <;!!DZ3fjg!owu71G1X9PfyKHaK4gx743wfZ0hYOiQAFtYUdvvp0C0usvbyaSDhFFjgVPx7DkWMsg$>)
> as described in the tutorial.
> It works really well when you have only HIS, ASP and GLU as titratable
> residues on the system (the occupancy vector of these residues is described
> with two numbers). When you have CYS (1 number) or LYS (3 numbers) it gives
> you a python error:
> RuntimeError: dictionary keys changed during iteration
> Does someone that has more python knowledge than me knows how this could
> be fixed?
> Thanks,
> ingrid

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST