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 ?
Many thanks
Garry
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