Is there a bug on waterbridge atom index?

[freeenergylab]

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!

[fkaiserbio]

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?