[gmx-users] Not enough ref_t and tau_t values!

Miguel Ortiz Lombardia molatwork at yahoo.es
Tue Mar 7 15:23:54 CET 2006

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Thank you Tsjerk.

Indeed, you're right. I'm using ffamber99, where the terminal residues
have names starting with N or C, for N- and C-terminal. After reading
your e-mail I re-run make_ndx and noticed that these terminal residues
are not considered Protein, making grompp complain for the reason you

Also, thank you for your advice on the bath. I'll follow it, of course.



Tsjerk Wassenaar wrote:
> Hi Miguel,
>     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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- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: molatwork at yahoo.es
www: http://www.ysbl.york.ac.uk/~mol/
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Dans les jardins mal fréquentés!
                                                       Georges Brassens
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