gromacs-data 5.0.2-1 / usr / share / gromacs / top / charmm27.ff / dna.rtp

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/usr/share/gromacs/top/charmm27.ff/dna.rtp is in gromacs-data 5.0.2-1.

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The actual contents of the file can be viewed below. 

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[ bondedtypes ] 
; Column 1 : default bondtype
; Column 2 : default angletype
; Column 3 : default proper dihedraltype
; Column 4 : default improper dihedraltype
; Column 5 : This controls the generation of dihedrals from the bonding.
;            All possible dihedrals are generated automatically. A value of
;            1 here means that all these are retained. A value of
;            0 here requires generated dihedrals be removed if
;              * there are any dihedrals on the same central atoms
;                specified in the residue topology, or
;              * there are other identical generated dihedrals
;                sharing the same central atoms, or
;              * there are other generated dihedrals sharing the
;                same central bond that have fewer hydrogen atoms
; Column 6 : number of neighbors to exclude from non-bonded interactions
; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
;            0 = do not generate such
; Column 8 : 1 = remove proper dihedrals if found centered on the same
;                bond as an improper dihedral
;            0 = do not generate such
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih 
     1       5          9        2        1           3      1     0 

;  =====================================================================
;  DNA 

;-----------------------------------------------------------------------
[ DA ]
;             H61  H62;
;               \  /
;                N6
;                |
;                C6
;              //  \
;              N1   C5--N7\\
;              |    ||     C8-H8
;              C2   C4--N9/
;             / \\ /     \
;           H2   N3       \
;                          \
;                           \
;                            \
;        O1P   H5'1 H4'  O4'  \
;         |      |    \ /   \  \
;        -P-O5'-C5'---C4'    C1'
;         |      |     \     / \
;        O2P    H5'2   C3'--C2' H1'
;                    / \    / \
;                 O3' H3' H2'1 H2'2
;                  |  
;                     
;
[ atoms ]
P	P	 1.50	0
O1P	ON3	-0.78	1
O2P	ON3	-0.78	2
O5'	ON2	-0.57	3
C5'	CN8B	-0.08	4
H5'1	HN8	 0.09	5
H5'2	HN8	 0.09	6
C4'	CN7	 0.16	7
H4'	HN7	 0.09	8
O4'	ON6	-0.50	9
C1'	CN7B	 0.16	10
H1'	HN7	 0.09	11
N9	NN2	-0.05	12
C5	CN5	 0.28	13
N7	NN4	-0.71	14
C8	CN4	 0.34	15
H8	HN3	 0.12	16
N1	NN3A	-0.74	17
C2	CN4	 0.50	18
H2	HN3	 0.13	19
N3	NN3A	-0.75	20
C4	CN5	 0.43	21
C6	CN2	 0.46	22
N6	NN1	-0.77	23
H61	HN1	 0.38	24
H62	HN1	 0.38	25
C2'	CN8	-0.18	26
H2'1	HN8	 0.09	27
H2'2	HN8	 0.09	28
C3'	CN7	 0.01	29
H3'	HN7	 0.09	30
O3'	ON2	-0.57	31
[ bonds ]
-O3'     P
P	O1P
P	O2P
P	O5'
O5'	C5'
C5'	C4'
C4'	O4'
C4'	C3'
O4'	C1'
C1'	N9
C1'	C2'
N9	C4
N9	C8
C4	N3
C2	N1
C6	N6
N6	H61
N6	H62
C6	C5
C5	N7
C2'	C3'
C3'	O3'
C1'	H1'
C2'	H2'1
C2'	H2'2
C3'	H3'
C4'	H4'
C5'	H5'1
C5'	H5'2
C8	H8
C2	H2
N1	C6
C2	N3
C4	C5
N7	C8
[ impropers ]
N6	C6	H61	H62
C6	N1	C5	N6

;--------------------------------------------------------------------------
[ DC ]
;
;                      H42  H41
;                        \  /    
;                         N4
;                         |
;                         C4
;                        /  \\
;                    H5-C5   N3
;                       ||   |
;                    H6-C6   C2
;                        \  / \\
;                         N1   O2
;                          \
;                           \
;                            \ 
;        O1P    H5'1H4'  O4'  \
;         |      |    \ /   \  \
;        -P-O5'-C5'---C4'    C1'
;         |      |     \     / \
;        O2P    H5'2  C3'--C2' H1'
;                    / \    / \
;                 O3' H3' H2'1 H2'2
;                   |  
;                     
[ atoms ]
P	P	 1.50	0
O1P	ON3	-0.78	1
O2P	ON3	-0.78	2
O5'	ON2	-0.57	3
C5'	CN8B	-0.08	4
H5'1	HN8	 0.09	5
H5'2	HN8	 0.09	6
C4'	CN7	 0.16	7
H4'	HN7	 0.09	8
O4'	ON6	-0.50	9
C1'	CN7B	 0.16	10
H1'	HN7	 0.09	11
N1	NN2	-0.13	12
C6	CN3	 0.05	13
H6	HN3	 0.17	14
C5	CN3	-0.13	15
H5	HN3	 0.07	16
C2	CN1	 0.52	17
O2	ON1C	-0.49	18
N3	NN3	-0.66	19
C4	CN2	 0.65	20
N4	NN1	-0.75	21
H41	HN1	 0.37	22
H42	HN1	 0.33	23
C2'	CN8	-0.18	24
H2'1	HN8	 0.09	25
H2'2	HN8	 0.09	26
C3'	CN7	 0.01	27
H3'	HN7	 0.09	28
O3'	ON2	-0.57	29
[ bonds ]
-O3'     P
P	O1P
P	O2P
P	O5'
O5'	C5'
C5'	C4'
C4'	O4'
C4'	C3'
O4'	C1'
C1'	N1
C1'	C2'
N1	C2
N1	C6
C2	N3
C4	N4
N4	H41
N4	H42
C4	C5
C2'	C3'
C3'	O3'
C1'	H1'
C2'	H2'1
C2'	H2'2
C3'	H3'
C4'	H4'
C5'	H5'1
C5'	H5'2
C5	H5
C6	H6
C2	O2
C5	C6
N3	C4
[ impropers ]
C2	N1	N3	O2
C4	N3	C5	N4
N4	C4	H41	H42

; --------------------------------------------------------------------
[ DG ]
;               O6
;               ||   
;               C6    
;              /  \  
;          H1-N1   C5--N7\\
;             |    ||     C8-H8
;             C2   C4--N9/
;            / \\ /      \
;      H21-N2   N3        \
;          |               \
;         H22               \
;                            \
;        O1P    H5'1 H4'  O4'  \
;         |      |    \ /   \  \
;        -P-O5'-C5'---C4'    C1'
;         |      |     \     / \
;        O2P    H5'2   C3'--C2' H1'
;                    / \    / \
;                 O3' H3' H2'1 H2'2
;                  |  
;                     
[ atoms ]
P	P	 1.50	0
O1P	ON3	-0.78	1
O2P	ON3	-0.78	2
O5'	ON2	-0.57	3
C5'	CN8B	-0.08	4
H5'1	HN8	 0.09	5
H5'2	HN8	 0.09	6
C4'	CN7	 0.16	7
H4'	HN7	 0.09	8
O4'	ON6	-0.50	9
C1'	CN7B	 0.16	10
H1'	HN7	 0.09	11
N9	NN2B	-0.02	12
C4	CN5	 0.26	13
N2	NN1	-0.68	14
H21	HN1	 0.32	15
H22	HN1	 0.35	16
N3	NN3G	-0.74	17
C2	CN2	 0.75	18
N1	NN2G	-0.34	19
H1	HN2	 0.26	20
C6	CN1	 0.54	21
O6	ON1	-0.51	22
C5	CN5G	 0.00	23
N7	NN4	-0.60	24
C8	CN4	 0.25	25
H8	HN3	 0.16	26
C2'	CN8	-0.18	27
H2'1	HN8	 0.09	28
H2'2	HN8	 0.09	29
C3'	CN7	 0.01	30
H3'	HN7	 0.09	31
O3'	ON2	-0.57	32
[ bonds ]
-O3'     P
P	O1P
P	O2P
P	O5'
O5'	C5'
C5'	C4'
C4'	O4'
C4'	C3'
O4'	C1'
C1'	N9
C1'	C2'
N9	C4
N9	C8
C4	N3
C2	N2
C2	N1
N2	H21
N2	H22
N1	H1
N1	C6
C6	C5
C5	N7
C2'	C3'
C3'	O3'
C1'	H1'
C2'	H2'1
C2'	H2'2
C3'	H3'
C4'	H4'
C5'	H5'1
C5'	H5'2
C8	H8
C2	N3
C4	C5
N7	C8
C6	O6
[ impropers ]
C2	N3	N1	N2
C6	N1	C5	O6
N2	H21	C2	H22

;---------------------------------------------------------------------- 
[ DT ]
;                  H51    O4
;                   |     ||
;               H52-C5M   C4    H3
;                   |  \ /  \  /
;                  H53  C5   N3
;                       ||   |
;                    H6-C6   C2
;                        \  / \\  
;                         N1   O2
;                          \
;                           \
;                            \ 
;        O1P    H5'1H4'  O4'  \
;         |      |    \ /   \  \
;        -P-O5'-C5'---C4'    C1'
;         |      |     \     / \
;        O2P    H5'2  C3'--C2' H1'
;                    / \    / \
;                 O3' H3' H2'1 H2'2
;                   |  
;                     
;
[ atoms ]
P	P	 1.50	0
O1P	ON3	-0.78	1
O2P	ON3	-0.78	2
O5'	ON2	-0.57	3
C5'	CN8B	-0.08	4
H5'1	HN8	 0.09	5
H5'2	HN8	 0.09	6
C4'	CN7	 0.16	7
H4'	HN7	 0.09	8
O4'	ON6	-0.50	9
C1'	CN7B	 0.16	10
H1'	HN7	 0.09	11
N1	NN2B	-0.34	12
C6	CN3	 0.17	13
H6	HN3	 0.17	14
C2	CN1T	 0.51	15
O2	ON1	-0.41	16
N3	NN2U	-0.46	17
H3	HN2	 0.36	18
C4	CN1	 0.50	19
O4	ON1	-0.45	20
C5	CN3T	-0.15	21
C5M	CN9	-0.11	22
H51	HN9	 0.07	23
H52	HN9	 0.07	24
H53	HN9	 0.07	25
C2'	CN8	-0.18	26
H2'1	HN8	 0.09	27
H2'2	HN8	 0.09	28
C3'	CN7	 0.01	29
H3'	HN7	 0.09	30
O3'	ON2	-0.57	31
[ bonds ]
-O3'     P
P	O1P
P	O2P
P	O5'
O5'	C5'
C5'	C4'
C4'	O4'
C4'	C3'
O4'	C1'
C1'	N1
C1'	C2'
N1	C2
N1	C6
C2	N3
N3	H3
N3	C4
C4	C5
C5	C5M
C2'	C3'
C3'	O3'
C1'	H1'
C2'	H2'1
C2'	H2'2
C3'	H3'
C4'	H4'
C5'	H5'1
C5'	H5'2
C6	H6
C5M	H51
C5M	H52
C5M	H53
C2	O2
C4	O4
C5	C6
[ impropers ]
C2	N1	N3	O2
C4	N3	C5	O4
C5	C4	C6	C5M

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