/usr/share/gromacs/top/atommass.dat is in gromacs-data 4.5.5-2.
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 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 | ; NOTE: longest names match
; General atoms
; '???' or '*' matches any residue name
??? H 1.00790
??? He 4.00260
??? Li 6.94100
??? Be 9.01220
??? B 10.81100
??? C 12.01070
??? N 14.00670
??? O 15.99940
??? F 18.99840
??? Ne 20.17970
??? Na 22.98970
??? Mg 24.30500
??? Al 26.98150
??? Si 28.08550
??? P 30.97380
??? S 32.06500
??? Cl 35.45300
??? Ar 39.94800
??? K 39.09830
??? Ca 40.07800
??? Sc 44.95590
??? Ti 47.86700
??? V 50.94150
??? Cr 51.99610
??? Mn 54.93800
??? Fe 55.84500
??? Co 58.93320
??? Ni 58.69340
??? Cu 63.54600
??? Zn 65.39000
??? Ga 69.72300
??? Ge 72.64000
??? As 74.92160
??? Se 78.96000
??? Br 79.90400
??? Kr 83.80000
??? Rb 85.46780
??? Sr 87.62000
??? Y 88.90590
??? Zr 91.22400
??? Nb 92.90640
??? Mo 95.94000
??? Tc 98.00000
??? Ru 101.07000
??? Rh 102.90550
??? Pd 106.42000
??? Ag 107.86820
??? Cd 112.41100
??? In 114.81800
??? Sn 118.71000
??? Sb 121.76000
??? Te 127.60000
??? I 126.90450
??? Xe 131.29300
??? Cs 132.90550
??? Ba 137.32700
??? La 138.90550
??? Ce 140.11600
??? Pr 140.90770
??? Nd 144.24000
??? Pm 145.00000
??? Sm 150.36000
??? Eu 151.96400
??? Gd 157.25000
??? Tb 158.92530
??? Dy 162.50000
??? Ho 164.93030
??? Er 167.25900
??? Tm 168.93420
??? Yb 173.04000
??? Lu 174.96700
??? Hf 178.49000
??? Ta 180.94790
??? W 183.84000
??? Re 186.20700
??? Os 190.23000
??? Ir 192.21700
??? Pt 195.07800
??? Au 196.96650
??? Hg 200.59000
??? Tl 204.38330
??? Pb 207.20000
??? Bi 208.98040
??? Po 209.00000
??? At 210.00000
??? Rn 222.00000
??? Fr 223.00000
??? Ra 226.00000
??? Ac 227.00000
??? Th 232.03810
??? Pa 231.03590
??? U 238.02890
??? Np 237.00000
??? Pu 244.00000
??? Am 243.00000
??? Cm 247.00000
??? Bk 247.00000
??? Cf 251.00000
??? Es 252.00000
??? Fm 257.00000
??? Md 258.00000
??? No 259.00000
??? Lr 262.00000
??? Rf 261.00000
??? Db 262.00000
??? Sg 266.00000
??? Bh 264.00000
??? Hs 277.00000
??? Mt 268.00000
; Proteins
; all hydrogen masses for proteins are added to the heavy atoms
; set all dummy masses to zero: the masses are now in the atoms
AAA MN1 0.0
AAA MN2 0.0
LYS MNZ1 0.0
LYS MNZ2 0.0
LYSH MNZ1 0.0
LYSH MNZ2 0.0
TYR MW 0.0
; This is for the N-terminus (H1 is summed into the N)
AAA H2 1.008
AAA H3 1.008
AAA CA 13.0190
AAA CB 14.0270
AAA CG 14.0270
AAA CD 13.0190
AAA CE 13.0190
AAA CH 13.0190
AAA CZ 13.0190
AAA N 15.0147
AAA OG 15.9994
AAA OH 15.9994
AAA SG 32.0600
ALA CB 15.0350
ARG CD 14.0270
ARG CZ 12.0110
ARG NH 16.0227
ASN ND 16.0227
ASN CG 12.0110
ASP CG 12.0110
ASPH OD2 17.0074
CYS SG 33.068
GLN CD 12.0110
GLN NE 16.0227
GLU CD 12.0110
GLUH OE2 17.0074
HIS CG 12.0110
HISA NE 14.0067
HISB ND 14.0067
HIS1 NE 14.0067
ILE CB 13.0190
ILE CD 15.0350
ILE CG2 15.0350
LEU CD 15.0350
LEU CG 13.0190
LYS CD 14.0270
LYS CE 14.0270
LYS NZ 16.0227
LYSH NZ 17.0307
MET CE 15.0350
PHE CG 12.0110
PRO N 14.0067
PRO CD 14.0270
SER OG 17.0074
THR CB 13.0190
THR CG 15.0350
THR OG 17.0074
TRP CD2 12.0110
TRP CE2 12.0110
TRP CG 12.0110
TYR CG 12.0110
TYR CZ 12.0110
TYR OH 17.0074
VAL CB 13.0190
VAL CG 15.0350
; water
SOL OW 15.9994
SOL HW 1.008
SOL MW 0.0
SOL LP 0.0
; DMSO
DMSO CD 15.03500
DMSO SD 32.06000
DMSO OD 15.99940
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