[gmx-developers] Gromacs pdb formatting

Mark Abraham mark.abraham at anu.edu.au
Tue Aug 3 05:24:55 CEST 2010

----- Original Message -----
From: Berk Hess <hess at cbr.su.se>
Date: Tuesday, August 3, 2010 1:40
Subject: [gmx-developers] Gromacs pdb formatting
To: Discussion list for GROMACS development <gmx-developers at gromacs.org>

> Hi,
> 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.

Following external standards always seems like a good idea to me. Updating 3rd-party scripts to regexp-match (?:ATOM  |HETATM) (or whatever) seems a simple enough change to demand.


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