[gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

Robert Johnson bobjohnson1981 at gmail.com
Wed Jun 13 23:54:34 CEST 2007

I could understand if it was doing this within pdb2gmx or something
that was constructing a topology file. I'm observing this behavior
when using editconf to simply convert files to another format or apply
box dimensions etc. Anyway, I submitted a bugzilla about it. This
isn't such a big problem - make of it what you will. ;-)

On 6/13/07, Erik Lindahl <lindahl at cbr.su.se> wrote:
> Hi Robert,
> On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote:
> > These are all fine points. However, the question I'm asking is why do
> > Gromacs tools change atoms named OXT in PDB files to O2? Of course
> > there are always workarounds i.e. just simply change the atom name in
> > the coordinate file. However, I was wondering if anyone knew why this
> > happened. I suppose I will submit a bugzilla.
> Don't bother for now :-)
> This is because of a few old brain-dead choices in pdb2gmx, but we're
> working on replacing that completely, and then we'll be name-agnostic.
> The only thing I can say in our defense is that most other programs
> also push their own naming convention when generation hydrogens, etc.
> For instance, charmm will rename the resname of the first/last few
> atoms in each chain to NTER/CTER.
> Cheers,
> Erik
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