[gmx-developers] Gromacs pdb formatting
feenstra at few.vu.nl
Mon Aug 9 19:20:24 CEST 2010
On 03/08/10 10:20, Berk Hess wrote:
> David van der Spoel wrote:
>> 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
>>> > 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?
> This is only the removal of excessive TER prints.
> We're waiting for feedback on the HETATM issue before committing that.
> We are only (and always) committing in release-4-5-patches.
> A git merge into master can be done at any time.
Are there any compatiblity issues re other tools used to read the
gromacs PDB files that would be fixed by this change?
I've always found the distinction between ATOM and HETATM very silly.
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam |
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| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
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