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

CC BY-SA 4.0
2022-04-29T09:43:05.910Z
2022-04-29T09:43:05.910Z
Matteo Ferla
<p>I have a PDB file in which the indexes of atoms are repeated (or better say refreshed) every 99999.</p>
<p>I am using MDtraj software to analyze this pdf file, so these repeating indexes cause some problems.</p>
<p>Does everyone encounter this problem and how can I fix it?</p>

<pdb>
Repeating indexes of atoms in PDB file
# Repeating indexes of atoms in PDB file

(Asked by: username_0 on 2022-04-29)

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?

**Tags:** pdb

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## 1 answers

### Answer by username_1 on 2022-04-29. Score: 1

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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