[gmx-developers] Gromacs pdb formatting

Berk Hess hess at cbr.su.se
Mon Aug 2 17:40:16 CEST 2010


We are trying to make Gromacs write more correct pdb output.
The current 4.5 beta writes TER after every molecule, but that's too much.
The next beata will write TER after protein, dna or rna chains and
mutiple residue molecules.

But atoms in other molecules, such as water and ions should be written
in HETATM fields,
not ATOM as Gromacs has always done and currently still does.

All Gromacs programs read HETATM just like ATOM.
I myself would have to update some of my personal scripts to also read ATOM.

Before changing such a common output file format, we would like to ask
the opinion of the users
on the change from ATOM to HETATM.


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