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I have a PDB file in which the indexes of atoms are repeated (or better say refreshed) every 99999.

I am using MDtraj software to analyze this pdf file, so these repeating indexes cause some problems.

Does everyone encounter this problem and how can I fix it?

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1 Answer 1

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Inconsistencies like randomly repeated atom indices, maxed out indices at 99999, integer overflowing indices to the negatives (yup, there's a program that has this bug), bad spacing, jumbled order etc. in a PDB are tolerated differently in different programs. Some will carp at missing atoms or non-standard atom names, which are not formatting errors.

In terms of atom indices, these are used in CONECT entries, but several programs bond by proximity or by known topology —CONECT entries are absent for canonical amino acids. Repeated residue indices and chain letter repeats cause issues with LINK and often with peptide chain sequence.

However, in a multimodel PDB the numbers in each model are expected to be reset at every MODEL so if the atom indices reset after the end of a model this is 100% expected.

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