[gmx-developers] Gromacs pdb formatting

[David van der Spoel]

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.
>
> Mark
>
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