CNT creation having more than 999 atoms

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Hello,
I’m facing an issue while creating a CNT with more than 999 atoms. Since the PDB format restricts the atom name/serial number field to 4 characters, once it goes beyond C999, the numbering gets truncated and random values are assigned. This is causing errors. Can anyone suggest a solution for handling CNT structures with more than 999 atoms?

2

Only print the last three digits of the number.

3

But the sequence will repeat. We need to have unique no for each atom.

4

Is it unclear what you are referring to. The atom number field has 5 digits, the residue number 4. None have only 3.

The atom numbers are ignored completely by GROMACS. Atoms are renumbered consecutively from 1. Residues are recognized by a change in residue number. Repeats are fine, as long as consecutive residues have different numbers.