gromacs-data 2018.1-1 / usr / share / gromacs / top / gromos45a3.ff / aminoacids.n.tdb

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/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb is in gromacs-data 2018.1-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

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[ None ]

[ NH3+ ]
[ replace ]
N		NL	14.0067	0.129
CA		CH1	13.019	0.127	0
[ add ]
3	4	H	N	CA	C
	H	1.008	0.248
[ delete ]
H
[ bonds ]
N	H1	gb_2
N	H2	gb_2
N	H3	gb_2
[ angles ]
H1	N	H2	ga_9
H2	N	H3	ga_9
H3	N	H1	ga_9
CA	N	H1	ga_10
CA	N	H2	ga_10
CA	N	H3	ga_10
[ dihedrals ]
H1	N	CA	C	gd_14

[ NH2 ]
[ replace ]
N		NL	14.0067	-0.83
[ add ]
2	4	H	N	CA	C
	H	1.008	0.415
[ delete ]
H
[ bonds ]
N	H1	gb_2
N	H2	gb_2
[ angles ]
H1	N	H2	ga_9
CA	N	H1	ga_10
CA	N	H2	ga_10
[ dihedrals ]
H1	N	CA	C	gd_14

[ PRO-NH2+ ]
[ replace ]
N		NT	14.0067	0.2
[ add ]
2	4	H	N	CA	C
	H	1.008	0.4
[ bonds ]
N	H1	gb_2
N	H2	gb_2
[ angles ]
H1	N	H2	ga_9
CA	N	H1	ga_10
CA	N	H2	ga_10
CD	N	H1	ga_10
CD	N	H2	ga_10
[ dihedrals ]
H1	N	CA	C	gd_14

[ PRO-NH ]
[ replace ]
N		N	14.0067	-0.28
[ add ]
1	4	H	N	CA	C
	H	1.008	0.28
[ bonds ]
N	H	gb_2
[ angles ]
CA	N	H	ga_10
CD	N	H	ga_10

[ GLY-NH3+ ]
[ replace ]
N		NL	14.0067	0.129
CA		CH2	14.027	0.127	0
[ add ]
3	4	H	N	CA	C
	H	1.008	0.248
[ delete ]
H
[ bonds ]
N	H1	gb_2
N	H2	gb_2
N	H3	gb_2
[ angles ]
H1	N	H2	ga_9
H2	N	H3	ga_9
H3	N	H1	ga_9
CA	N	H1	ga_10
CA	N	H2	ga_10
CA	N	H3	ga_10
[ dihedrals ]
H1	N	CA	C	gd_14

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