/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb 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 | [ None ]
[ GLY-NH3+ ]
[ replace ]
N opls_287 14.0027 -0.3
CA opls_292B 12.011 0.19
[ add ]
3 4 H N CA C
opls_290 1.008 0.33
[ delete ]
H
[ GLY-ZWITTERION_NH3+ ]
[ replace ]
N opls_287 14.0027 -0.3
CA opls_298 12.011 0.09
[ add ]
3 4 H N CA C
opls_290 1.008 0.33
[ delete ]
H
[ PRO-NH2+ ]
[ replace ]
N opls_309 14.0027 -0.2
CA opls_246 12.011 0.23
CD opls_296 12.011 0.17
[ add ]
2 4 H N CA C
opls_310 1.008 0.31
[ PRO-ZWITTERION_NH2+ ]
[ replace ]
N opls_309 14.0027 -0.2
CA opls_246 12.011 0.13
CD opls_296 12.011 0.17
[ add ]
2 4 H N CA C
opls_310 1.008 0.31
[ NH3+ ]
[ replace ]
N opls_287 14.0027 -0.3
CA opls_293B 12.011 0.25
[ add ]
3 4 H N CA C
opls_290 1.008 0.33
[ delete ]
H
[ ZWITTERION_NH3+ ]
[ replace ]
N opls_287 14.0027 -0.3
CA opls_299 12.011 0.15
[ add ]
3 4 H N CA C
opls_290 1.008 0.33
[ delete ]
H
[ GLY-NH2 ]
[ replace ]
N opls_900 14.0027 -0.9
CA opls_906B 12.011 0.06
[ add ]
2 4 H N CA C
opls_909 1.008 0.36
[ delete ]
H
[ PRO-NH ]
[ replace ]
N opls_901 14.0027 -0.78
CA opls_246 12.011 0.14
CD opls_245 12.011 0.08
[ add ]
1 4 H N CA C
opls_910 1.008 0.38
[ NH2 ]
[ replace ]
N opls_900 14.0027 -0.9
CA opls_912B 12.011 0.12
[ add ]
2 4 H N CA C
opls_909 1.008 0.36
[ delete ]
H
|