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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