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

From: Brian Radak (
Date: Fri Dec 10 2021 - 16:01:10 CST

I do not know the exact issue, but this is almost definitely due to the
hasty and outdated conversion to python 3 from several years back. The
only solution I can recommend right now is to use conda (or some such)
to go back to an older version of python (as far back as 3.6 might be
necessary). I will see if I can clean things up for the 3.6+ modern age,
but I can't promise a quick timeline for that (this is entirely a side
project for me these days).



On 12/10/21 1:28 PM, Brian Radak wrote:
> 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.
> Cheers,
> Brian
> 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!qDnHjHsAWog1gTK9_km1uxmjVtFA0q-J6glu5aPJkBR209zcVQ79Bc64PdD_7DbrrQ$
> <;!!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

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