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pharmai / plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

Home Page:http://plip.biotec.tu-dresden.de

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Is there a bug on waterbridge atom index?

freeenergylab opened this issue · comments

commented

Hey here,

report.txt
complex.pdb.txt

I renamed the complex.pdb to complex.pdb.txt here so that I can upload this file on GitHub here.

For ligand called L1, the waterbridge interactions have inconsistent atom index in report.txt with those in complex.pdb.
Is there a bug about it?

Thanks!

commented

Hi,

PLIP pre-processes and, if necessary, protonates the input. This could change the atom numbering. Did PLIP generate a plipfixed PDB file? And what was the exact command line call you issued?