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

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Thu Feb 20 12:48:11 CET 2014

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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