The element symbols on the right should be in positions 77-78, or 3
positions to the right. When they’re present, they take precedence over the
atom name columns, because deciphering Na = sodium vs. Na = nitrogen alpha
is a pain.
Also, for what it’s worth, these should definitely be HETATM not
I believe if you shift the Na and Cl atom names one step to the left, (column
14 to 13), andinsert a space after the atom name, as in:
from:
123456789012345678901234567890123456789012345678901234567890
ATOM 1 Na Na 1 0.000 0.000 0.000 1.00 0.00 NaATOM
2 Cl
Hi, I think I have a correct pdb file here, containing Sodium Chloride
TITLE MOL processed by ACT - The Alexandria Chemistry Tookit
REMARKTHIS IS A SIMULATION BOX
CRYST1 28.200 28.200 28.200 90.00 90.00 90.00 P 1 1
MODEL1
ATOM 1 NaNa1
