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

[garry]

Dear Justin
Many thanks for this...all is now well.
Best
Garry

On 24 Oct 2008, at 20:42, Justin A. Lemkul wrote:

> 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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