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pfa file required using residue-based fda_shortest_path #49

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BerndDoser opened this issue Oct 17, 2022 · 2 comments
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pfa file required using residue-based fda_shortest_path #49

BerndDoser opened this issue Oct 17, 2022 · 2 comments
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@BerndDoser
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I'm trying to use the fda_shortest_path module for the analysis with the following comand

gmx_fda fda_shortest_path -i output.pfr -s md.tpr -n index.ndx -o shortest.pdb

and I receive the following error message:

Fatal error:
Error opening file fda.pfa

If you notice from my input file, I performed the analysis residue-based and not atom-based, thus I only have an output.pfr file and not a out.pfa.
As a test, I created an empity fda.pfa file and the analysis work without printing anything in the output.
I suppose this could be due to a problem in the code because it seems the algo requires a specific file called fda.pfa

@BerndDoser BerndDoser self-assigned this Oct 17, 2022
@BerndDoser BerndDoser added the bug label Oct 17, 2022
@BerndDoser
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BerndDoser commented Oct 19, 2022

Unfortunately, I cannot reproduce the issue with

cd src/gromacs/gmxana/fda/tests/data/glycine_trimer
gmx_fda fda_shortest_path -i fda.pfr -s glycine_trimer.pdb -n index.ndx -o shortest.pdb

@BerndDoser BerndDoser added verify Reproduce the reported behavior and removed bug labels Oct 19, 2022
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The issue was reproducible with special user data. Although the -diff option is not used, the program is trying to open a second pairwise forces file, which is not available.

@BerndDoser BerndDoser added bug and removed verify Reproduce the reported behavior labels Oct 19, 2022
@BerndDoser BerndDoser added this to the 2.11 milestone Oct 19, 2022
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