Garry,<br><br>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.<br>
<br>Andy<br><br>garry wrote:<br>
><br>
> I am a novice at Gromacs (although I used Gromos 20+ years ago!)....I<br>
> have a dimer with two zincs per monomer, and I get the following<br>
> complaint when running the grompp with pr.dmp, which I assume is<br>
> referring to the 4 zincs.<br>
><br>
><br>
> There are: 6789 OTHER residues<br>
> There are: 262 PROTEIN residues<br>
> There are: 0 DNA residues<br>
> Analysing Protein...<br>
> Analysing Other...<br>
><br>
> ------------------------------<div id=":zw" class="ArwC7c ckChnd">-------------------------<br>
> Program grompp, VERSION 3.3.2<br>
> Source code file: readir.c, line: 865<br>
><br>
> Fatal error:<br>
> 4 atoms are not part of any of the T-Coupling groups<br>
> -------------------------------------------------------<br>
><br>
> the zincs are in the pdb file as (properly formatted in the pdb file!):<br>
><br>
> ATOM 2103 SG CYS B 133 -10.574 -5.438 18.502 1.00<br>
> 51.42 S<br>
> ATOM 2104 C CYS B 133 -10.084 -9.287 20.134 1.00<br>
> 50.50 C<br>
> ATOM 2105 O CYS B 133 -9.171 -9.545 20.923 1.00<br>
> 50.69 O<br>
> HETATM 2106 ZN ZN2+C 1 -12.350 1.941 1.066 1.00<br>
> 43.80 ZN<br>
> HETATM 2107 ZN ZN2+C 2 -21.690 2.493 -3.958 1.00<br>
> 38.99 ZN<br>
> HETATM 2109 ZN ZN2+C 3 -11.783 11.509 10.159 1.00<br>
> 28.52 ZN<br>
> HETATM 2108 ZN ZN2+C 4 -17.911 8.618 18.155 1.00<br>
> 32.42 ZN<br>
><br>
> What am I doing wrong ?<br>
><br>
<br>
What does your .mdp file look like? Have you included the Zn2+ within one of<br>
your tc-grps?<br>
<br>
-Justin</div>