and then tried to make the index file again from the latter file. It
didn't work either. But I thought the problem might be in the 'pdb'
structure file produced by mdrun.
Could this happen?
No.
Is it possible that the three groups you give don't cover all the atoms in your system? Besides, don't couple a handful of sodium atoms to a private heat bath. Check the mailing lists... This has passed so many times. In your case, go for two groups: Protein and Non-Protein, for which you don't need an index file in the first place.
Cheers,
Miguel
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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