[gmx-users] atoms not part of any of the T-coupling groups

[Andy Shelley]

Garry,

I believe you are trying to not temperature couple the 4 zincs. To do this
put the 4 zincs in one group and include that group in the listing of
tc_grps and then correspondingly assign tau_t. tau_t=0 means no temperature
coupling, but I think you will also need to give a temperature for the
tau_t=0 even though that group does not have temperature coupling. See
section 7.3.13 in the gromacs user manual.

Andy

garry wrote:
>
> I  am a novice at Gromacs (although I used Gromos 20+ years ago!)....I
> have a dimer with two zincs per monomer, and I get the following
> complaint when running the grompp with pr.dmp, which I assume is
> referring to the 4 zincs.
>
>
> There are:  6789      OTHER residues
> There are:   262    PROTEIN residues
> There are:     0        DNA residues
> Analysing Protein...
> Analysing Other...
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3.2
> Source code file: readir.c, line: 865
>
> Fatal error:
> 4 atoms are not part of any of the T-Coupling groups
> -------------------------------------------------------
>
> the zincs are in the pdb file as (properly formatted in the pdb file!):
>
> ATOM   2103  SG  CYS B 133     -10.574  -5.438  18.502  1.00
> 51.42           S
> ATOM   2104  C   CYS B 133     -10.084  -9.287  20.134  1.00
> 50.50           C
> ATOM   2105  O   CYS B 133      -9.171  -9.545  20.923  1.00
> 50.69           O
> HETATM 2106 ZN   ZN2+C   1     -12.350   1.941   1.066  1.00
> 43.80          ZN
> HETATM 2107 ZN   ZN2+C   2     -21.690   2.493  -3.958  1.00
> 38.99          ZN
> HETATM 2109 ZN   ZN2+C   3     -11.783  11.509  10.159  1.00
> 28.52          ZN
> HETATM 2108 ZN   ZN2+C   4     -17.911   8.618  18.155  1.00
> 32.42          ZN
>
> What am I doing wrong ?
>

What does your .mdp file look like?  Have you included the Zn2+ within one
of
your tc-grps?

-Justin
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