[gmx-developers] Gromacs pdb formatting
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 3 10:18:24 CEST 2010
On 2010-08-03 05.24, Mark Abraham wrote:
> ----- 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.
I see there already is a patch to pdbio.c (by Erik) in
release-4-5-patches about this. Should this be merged in master too?
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
More information about the gromacs.org_gmx-developers