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

[Justin A. Lemkul]

Wouldn't it be better to couple the Protein and Zn2+ together (i.e., index group 
Protein_Zn2+)?  Coupling ions separately often leads to weird 
behavior/explosions when they're free in the solvent.  I've never dealt with 
proteins that have ions bound, so I'm curious to see what everyone else thinks 
about this, just as a point of curiosity.

-Justin

Andy Shelley wrote:
> 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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-- 
========================================

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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