[gmx-users] conversion xtc to xyz format with openbabel
Dr. Vitaly Chaban
vvchaban at gmail.com
Sat Feb 22 22:23:34 CET 2014
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
> Stéphane Abel, PhD
> CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
> Bat 528 Door 138C
> Gif-sur-Yvette, F-91191 FRANCE
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