/usr/share/gromacs/top/defselection.dat is in gromacs-data 4.6.5-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | protein = resname ABU ACE AIB ALA ARG ARGN ASN ASN1 ASP ASP1 ASPH
CYS CYS1 CYS2 CYSH DALA GLN GLU GLUH GLY
HIS HIS1 HISA HISB HISH HSD HSE HSP HYP ILE LEU
LYS LYSH MELEU MET MEVAL NAC NH2 PHE PHEH PHEU PHL
PRO SER THR TRP TRPH TRPU TYR TYRH TYRU VAL PGLU;
"Protein" protein;
"Protein-H" protein and not name "H*" "[0-9]?H.*";
"C-alpha" protein and name CA;
"Backbone" protein and name N CA C;
"MainChain" protein and name N CA C O O1 O2 OC1 OC2 OT OXT;
"MainChain+Cb" protein and name N CA CB C O O1 O2 OC1 OC2 OT OXT;
"MainChain+H" protein and name N CA C O O1 O2 OC1 OC2 OT OXT H1 H2 H3 H "[0-9]?H";
"SideChain" protein and not name N CA C O O1 O2 OT OXT H1 H2 H3 H "[0-9]?H";
"SideChain-H" protein and not name N CA C O O1 O2 OT OXT "H*" "[0-9]?H.*";
"Prot-Masses" protein and not name MN1 MN2 MCB1 MCB2 MCG1 MCG2 MCD1 MCD2 MCE1 MCE2 MNZ1 MNZ2;
"DNA" resname A T G C U;
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