Error loading data/trp file to new for mdanalysis 0.20?

[FriederikeBiermann]

Hey, I really want to use your tool, because it looks so convenient (and open source which I love). While installing I was only able to get pycontact to work with mdanalysis 0.20.1, because everytime I used the newer version 2.7, I would run into various problems (I was able to fix the MDAnalysis.core.Selection error myself, but even then, there was still a File "/home/friederike/anaconda3/lib/python3.9/site-packages/PyContact/core/aroundPatch.py", line 14, in class AroundSelection(DistanceSelection): NameError: name 'DistanceSelection' is not defined error). The problem now is, I can't get my files to be loaded in pycontact. I tried to run

>>> import MDAnalysis as mda
>>> u = mda.Universe("md_1.tpr")
/home/friederike/.local/lib/python3.10/site-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for md_1.tpr. Skipping this file.
  warnings.warn('No coordinate reader found for {}. Skipping '
>>> print(u.segments)
<SegmentGroup [<Segment seg_0_Protein_chain_A>, <Segment seg_1_Protein_chain_B>, <Segment seg_2_SOL>]>

But this only works in mdanalysis 2.7, otherwise it will give me this error: NotImplementedError: Your tpx version is 129, which this parser does not support, yet

I used segid seg_0_Protein_chain_A and segid seg_1_Protein_chain_B for the identifiers, my md_1.trp and the corresponding xtc file for pycontact, but I always get the error loading data message. Is it because I made a mistake with the seqids or because mdanalysis 0.20 can't actually read tpx v 129 files? Thank you so much in advance!! Best Frida

[FriederikeBiermann]

I fixed it myself by just copying the topology folder files related to trp parsing of mdanalysis 2.7 into the topology folder of mdanalysis 0.20 :)

[HOng7521]

Hi, I recently encountered the same issue as you did but unfortunately, copying the TPRParser.py and tpr folder from mdanalysis 2.7 to that of 0.20 didn't work. Can you kindly elaborate more on the steps you took? Thank you in advance.

[FriederikeBiermann]

Hi, if your issue persists, i can maybe just send you my mdanalysis + pycontact dirs :)

[FriederikeBiermann]

You have to adjust this to the TRP version you are actually using: https://github.com/MDAnalysis/mdanalysis/pull/4052/commits/d3e5d12a22554e2f4afcfa9951b2d04164330b93

[HOng7521]

Hi, thanks for getting back to me and for offering to share you mdanalysis + pycontact directories. . I did update the TPRParser.py to include newer versions of GROMACS (up to 2023) but that didn't work. I was wondering which version of MDAnalysis, PyContact (1.0.2 or develop version) and PyQt5 you had installed. We couldn't install version 1.0.2 but managed to install the develop version. Can you kindly share how you had installed PyContact? Thanks again.

[FriederikeBiermann]

Sure, I am using Pycontact 1.0.4, I am not sure if this is the develop version. Best Frida