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rdf_data not initialized properly when running solute.run() #101
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Thanks for the report. I think you are probably right about this. Could you post the input files so I can take a look? In the meantime, you could try using |
https://drive.google.com/drive/folders/1cdZyy6Cca2IfW2qwt9HVLevLtmYS_KH9?usp=sharing You can find the files here. Thank you for the suggestion, it worked! |
@orionarcher Were you able to fix it? |
Not yet but I've observed the bug in another case and it's on my TODO list. |
Hi Caboomi. I am taking a look at this but would appreciate some help. Would you mind sending along a minimal reproduction of the bug? In particular, could 1) you remove the calls to I don't have |
Hey I am really sorry! I just saw this! I tried reproducing the bug but it's fixed now! Thank you so much! |
I am using ase to convert an xdatcar file to a xyz and pdb file and reading it into the mda.Universe as you can see in the pdf attached
vertopal.com_5x_analysis.pdf. I am receiving an error when running solute.plot_solvation_radius('Li', solvent) as KeyError: 'Li' despite having this:
solute = Solute.from_atoms(
dme_Li,
{'dme_TFSI': dme_TFSI, 'dme_DOL': dme_DOL, 'dme_DME': dme_DME},
solute_name="Li",
radii={"dme_TFSI": 2.6, "dme_DOL": 2.6, "dme_DME": 2.6}
)
as my solute.
I think it could stem from run() not initializing rdf_data properly as it creates solute_0 ... solute_4 in my rdf_data rather than having 'Li'in the directory. My Li solute is made up of 5 Li atoms.
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