gromacs-data 4.5.5-2 / usr / share / gromacs / top / gmx2.ff / aminoacids.hdb

This file is indexed.

/usr/share/gromacs/top/gmx2.ff/aminoacids.hdb 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. 

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ACE     1       
3	4	HA	CA	C	O
ALA     3       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
3	4	HB	CB	CA	N
ARG     8       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
2	6	HG	CG	CD	CB
2	6	HD	CD	NE	CG
1	1	HE	NE	CD	CZ
2	3	HH1	NH1	CZ	NE
2	3	HH2	NH2	CZ	NE
ASN     4       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
2	3	HD2	ND2	CG	CB
ASP     3       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
ASPH    4       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
1	2	HD1	OD1	CG	CB
CYS2    3       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	SG	CA
CYSH    4       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	SG	CA
1	2	HG	SG	CB	CA
FAD     7       
2	3	HN6	AN6	AC6	AC5
1	2	HO2*	AO2*	AC2*	AC1*
1	2	HO3*	AO3*	AC3*	AC2*
1	2	H4*	O4*	C4*	C5*
1	2	H3*	O3*	C3*	C4*
1	2	H2*	O2*	C2*	C3*
1	2	H3	N3	C4	C4A
GLN     5       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
2	6	HG	CG	CD	CB
2	3	HE2	NE2	CD	CG
GLU     4       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
2	6	HG	CG	CD	CB
GLUH    5       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
2	6	HG	CG	CD	CB
1	2	HE2	OE2	CD	CG
GLY     2       
1	1	H	N	-C	CA
2	6	HA	CA	C	N
HEME    18      
3	4	HMA	CMA	C3A	C4A
3	4	HMB	CMB	C2B	C3B
3	4	HMC	CMC	C2C	C3C
3	4	HMD	CMD	C2D	C1D
3	4	HBC	CBC	CAC	C3C
2	6	HAC	CAC	C3C	CBC
2	6	HAB	CAB	CBB	C3B
3	4	HBB	CBB	CAB	C3B
1	1	HHC	CHC	C4B	C1C
1	1	HHD	CHD	C4C	C1D
1	1	HHB	CHB	C4A	C1B
1	1	HHA	CHA	C4D	C1A
2	6	HBA	CBA	CAA	CGA
2	6	HAA	CAA	CBA	C2A
2	6	HBD	CBD	CAD	CGD
2	6	HAD	CAD	CBD	C2D
1	4	H2A	O2A	CGA	CBA
1	4	H2D	O2D	CGD	CBD
HIS1    6       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
1	1	HD2	CD2	CG	NE2
1	1	HE1	CE1	ND1	NE2
1	1	HD1	ND1	CG	CE1
HISA    6       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
1	1	HD1	ND1	CG	CE1
1	1	HD2	CD2	CG	NE2
1	1	HE1	CE1	ND1	NE2
HISB    6       
1	1	H	N	-C	CA
2	6	HB	CB	CG	CA
1	5	HA	CA	N	C	CB
1	1	HE2	NE2	CE1	CD2
1	1	HD2	CD2	CG	NE2
1	1	HE1	CE1	ND1	NE2
HISH    7       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
1	1	HD2	CD2	CG	NE2
1	1	HE1	CE1	ND1	NE2
1	1	HD1	ND1	CG	CE1
1	1	HE2	NE2	CE1	CD2
HO4     1       
3	10	HW	OW
HOH     1       
2	7	HW	OW
HYP     3       
1	5	HA	CA	N	C	CB
1	2	HD1	OD1	CG	CB
1	5	HG	CG	CB	OD1	CD2
ILE     6       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
1	5	HB	CB	CA	CG1	CG2
2	6	HG1	CG1	CD	CB
3	4	HG2	CG2	CB	CA
3	4	HD	CD	CG1	CB
LEU     6       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
1	5	HG	CG	CB	CD1	CD2
3	4	HD1	CD1	CG	CB
3	4	HD2	CD2	CG	CB
LYS     7       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
2	6	HG	CG	CD	CB
2	6	HD	CD	CE	CG
2	6	HE	CE	NZ	CD
2	4	HZ	NZ	CE	CD
LYSH    7       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
2	6	HG	CG	CD	CB
2	6	HD	CD	CE	CG
2	6	HE	CE	NZ	CD
3	4	HZ	NZ	CE	CD
MET     5       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
2	6	HG	CG	SD	CB
3	4	HE	CE	SD	CG
NAC     2       
1	1	H	N	-C	CA
3	4	HA	CA	N	-C
NH2     1       
2	3	H	N	-C	-CA
OCT     8       
3	4	H1	C1	C2	C3
2	6	H2	C2	C1	C3
2	6	H3	C3	C2	C4
2	6	H4	C4	C3	C5
2	6	H5	C5	C4	C6
2	6	H6	C6	C5	C7
2	6	H7	C7	C6	C8
2	6	H8	C8	C7	O9
PHE     8       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
1	1	HD1	CD1	CG	CE1
1	1	HD2	CD2	CG	CE2
1	1	HE1	CE1	CD1	CZ
1	1	HE2	CE2	CD2	CZ
1	1	HZ	CZ	CE1	CE2
PRO     4       
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
2	6	HG	CG	CD	CB
2	6	HD	CD	N	CG
SER     4       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	OG	CA
1	2	HG	OG	CB	CA
TFE     1       
1	2	H	O	C2	C1
THR     5       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
1	5	HB	CB	CA	OG1	CG2
1	2	HG1	OG1	CB	CA
3	4	HG2	CG2	CB	CA
TRP     9       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
1	1	HD1	CD1	NE1	CG
1	1	HE1	NE1	CD1	CE2
1	1	HE3	CE3	CD2	CZ3
1	1	HZ3	CZ3	CE3	CH2
1	1	HH2	CH2	CZ3	CZ2
1	1	HZ2	CZ2	CE2	CH2
TYR     8       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
2	6	HB	CB	CG	CA
1	1	HD1	CD1	CG	CE1
1	1	HD2	CD2	CG	CE2
1	1	HE1	CE1	CD1	CZ
1	1	HE2	CE2	CD2	CZ
1	2	HH	OH	CZ	CE1
VAL     5       
1	1	H	N	-C	CA
1	5	HA	CA	N	C	CB
1	5	HB	CB	CA	CG1	CG2
3	4	HG1	CG1	CB	CA
3	4	HG2	CG2	CB	CA

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