[gmx-developers] Gromacs pdb formatting

[Berk Hess]

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
>> 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?
>
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.

Berk