/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn 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 | ; atom renaming specification
; residue gromacs forcefield
NALA H H1
NGLY H H1
NSER H H1
NTHR H H1
NLEU H H1
NILE H H1
NVAL H H1
NASN H H1
NGLN H H1
NARG H H1
NHID H H1
NHIE H H1
NHIP H H1
NTRP H H1
NPHE H H1
NTYR H H1
NGLU H H1
NASP H H1
NLYS H H1
NPRO H H1
NCYS H H1
NCYX H H1
NMET H H1
NGLH H H1
NASP H H1
; This mapping of O->OC2 and OXT->OC1 might look a bit strange,
; but when we rebuild an oxygen it will be placed directly after C, so
; this mapping makes sure OC1 comes before OC2. The oxygens are anyway chemically
; equivalent, and if you already had their coordinates present they will be kept intact.
CALA O OC2
CALA OXT OC1
CGLY O OC2
CGLY OXT OC1
CSER O OC2
CSER OXT OC1
CTHR O OC2
CTHR OXT OC1
CLEU O OC2
CLEU OXT OC1
CILE O OC2
CILE OXT OC1
CVAL O OC2
CVAL OXT OC1
CASN O OC2
CASN OXT OC1
CGLN O OC2
CGLN OXT OC1
CARG O OC2
CARG OXT OC1
CHID O OC2
CHID OXT OC1
CHIE O OC2
CHIE OXT OC1
CHIP O OC2
CHIP OXT OC1
CTRP O OC2
CTRP OXT OC1
CPHE O OC2
CPHE OXT OC1
CTYR O OC2
CTYR OXT OC1
CGLU O OC2
CGLU OXT OC1
CASP O OC2
CASP OXT OC1
CLYS O OC2
CLYS OXT OC1
CPRO O OC2
CPRO OXT OC1
CCYS O OC2
CCYS OXT OC1
CCYX O OC2
CCYX OXT OC1
CMET O OC2
CMET OXT OC1
CGLH O OC2
CGLH OXT OC1
CASH O OC2
CASH OXT OC1
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