[gmx-users] conversion xtc to xyz format with openbabel

[Mark Abraham]

On Sat, Feb 22, 2014 at 10:16 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> The workaround is to "trjconv -o 111.pdb", open an editor, select a
> block of coordinates, and paste in XYZ file.
>
> I also do not like PDB files from gromacs, but AFAIK many programs
> generate such PDB files which other programs refuse to read.
>

Yes, this is problematic. PDB was in active use before it had a spec, IIRC
:-) One problem implementing support for that in GROMACS is that you have
to *know* the element in order to write its symol, and this is very ugly to
support. Should we commit resources to writing and maintaining code to read
in databases to provide an imperfect mapping from reside and atom name to
element symbol for every supported force field? Or refuse to do editconf -f
in.gro -o out.pdb or trjconv -f in.trr -o out.pdb unless -s the.tpr is
supplied? Or accept that most tools probably cope with this particular
imperfection because there's lots of old tools that implement it? Or write
'X' in those fields and deal with complaints from users of tools who see
that the field is present and do not use whatever heuristics they have for
coping with the empty field, or whose PDB-format trajectories are now twice
as large because every ATOM line has thirty extra spaces and an X?

Mark


>
> Dr. Vitaly V. Chaban
>
>
> On Thu, Feb 20, 2014 at 12:47 PM, ABEL Stephane 175950
> <Stephane.ABEL at cea.fr> wrote:
> > Hello all,
> >
> > My apologies for these  out topic questions
> >
> >  Does anybody have already try to convert xtc trajectory into xyz with
> openbabel?
> >
> > Btw, it seems that pdb file generated with editconf can not be read by
> openbabel. I obtain the following error :
> >
> >  WARNING: Problems reading a PDB file
> >   Problems reading a HETATM or ATOM record.
> >   According to the PDB specification,
> >   columns 77-78 should contain the element symbol of an atom.
> >   but OpenBabel found '  ' (atom 1)
> >
> >
> > Does anybody have a workaround?
> >
> > Thanks in advance
> >
> >
> > --------
> > Stéphane Abel, PhD
> > CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
> > Bat 528 Door 138C
> > Gif-sur-Yvette, F-91191 FRANCE
> > Phone (portable) : +33 6 49 37 70 60
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