Problem was in io.f - specifically in the mmp file processing. The ratomid and the atomid were not being calculated correctly. atomid is relative to the specfic file being processed and ratomid is the real atom id for all atoms in all templates processed.
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The fix was tested against 4 molecule templates. The molecule numbering problem was fixed as well. The word "Molecule" has replaced "Chunk" in the MMP file. This will allow the user to see that the MMP file was generated by PACKMOL.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Problem was in io.f - specifically in the mmp file processing. The ratomid and the atomid were not being calculated correctly. atomid is relative to the specfic file being processed and ratomid is the real atom id for all atoms in all templates processed.
The fix was tested against 4 molecule templates. The molecule numbering problem was fixed as well. The word "Molecule" has replaced "Chunk" in the MMP file. This will allow the user to see that the MMP file was generated by PACKMOL.