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

[Justin A. Lemkul]

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

> Many thanks
> Garry
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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