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

[Dr. Vitaly Chaban]

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.


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
>
>
> --------
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