PDB FILE:

ATOM      1  N1  DA  A   1       3.153   1.193  -7.063  1.00  0.00           N
ATOM      2  C5' DA  A   1       2.969   1.740   0.995  1.00  0.00           C
ATOM      3  C3' DA  A   1       1.427   0.000   0.000  1.00  0.00           C
ATOM      4  N6  DA  A   1       5.408   0.773  -7.070  1.00  0.00           N
ATOM      5  O5' DA  A   1       3.981   0.794   0.965  1.00  0.00           O
ATOM      6  N9  DA  A   1       3.075   0.501  -3.140  1.00  0.00           N
ATOM      7  O4' DA  A   1       2.425   1.679  -1.308  1.00  0.00           O
ATOM      8  C2  DA  A   1       2.010   1.305  -6.388  1.00  0.00           C
ATOM      9  C6  DA  A   1       4.267   0.848  -6.405  1.00  0.00           C
ATOM     10  C4' DA  A   1       1.927   1.443   0.000  1.00  0.00           C
ATOM     11  N7  DA  A   1       5.076   0.266  -4.075  1.00  0.00           N
ATOM     12  C5  DA  A   1       4.158   0.625  -5.030  1.00  0.00           C
ATOM     13  N3  DA  A   1       1.796   1.121  -5.091  1.00  0.00           N
ATOM     14  C8  DA  A   1       4.381   0.222  -2.974  1.00  0.00           C
ATOM     15  C1' DA  A   1       2.090   0.618  -2.169  1.00  0.00           C
ATOM     16  C4  DA  A   1       2.924   0.772  -4.473  1.00  0.00           C
ATOM     17  C2' DA  A   1       1.995  -0.571  -1.283  1.00  0.00           C
ATOM     18  O3' DA  A   1       0.000   0.000   0.000  1.00  0.00           O

RTP FILE:

P	 P2		1.50   0
O1P  ON3   -0.78   1
O2P  ON3   -0.78   2
O5'  ON2   -0.57   3
C5'  CN8B  -0.08   4
H5'  HN8	0.09   5
H5'' 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'  HN8	0.09  27
H2'' 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'
C2'  H2''
C3'  H3'
C4'  H4'
C5'  H5'
C5'  H5''
C8	 H8
C2	 H2
N1	 C6
C2	 N3
C4	 C5
N7	 C8
[ impropers ]
N6	C6	H61 H62
C6	N1	C5	N6

TDB FILE:

[ None ]

[ GLY-NH3+ ]
[ replace ]
 N	 N	 NH3	 14.0070 -0.30
 CA  CA  CT2	 12.011   0.13
[ Add ]
 3	 4	 H		 N		 CA   C
	 HC  1.008	 0.33	 -1
[ delete ]
 HN

[ NH3+ ]
[ replace ]
 N	 N	 NH3	 14.0070 -0.30
 CA  CA  CT1	 12.011   0.21
 HA  HA  HB1	 1.008	  0.10
[ Add ]
 3	 4	 H		 N		 CA		 C
	 HC  1.008	 0.33	 -1
[ delete ]
 HN

[ PRO-NH2+ ]
[ replace ]
 N	 N	   NP	14.0070 -0.07
 CA  CA    CP1	12.011	 0.16
 CD  CD    CP3	12.011	 0.16
[ add ]
 2	 4	 HN		 N		 CA		 C
	 HC  1.008	 0.24	 -1

; Created by Michel Cuendet
[ NH2 ]
[ replace ]
 N		NH2    14.007  -0.96
 CA		CT1    12.011	0.19
 HA		HB1		1.008	0.09
[ add ]
 2	 4	 H		N		CA	C
	 H	 1.008	0.34	-1
[ delete ]
 HN

; CHARMM NGNE patch, new 
[ GLY-NH2 ]
[ replace ]
 N		NH2		14.007 -0.96
 CA		CT2		12.011	0.10
 HA1	HB2		 1.008	0.09
 HA2	HB2		 1.008	0.09
[ add ]
 2	4	H		N		CA	C
	H	1.008	0.34	-1
[ delete ]
 HN

; Created by Bjelkmar 
[ PRO-NH ]
[ replace ]
 N		NP	14.0070 -0.40
 CA		CP1 12.011	-0.08
 CD		CP3 12.011	-0.10
[ add ]
 1	4	H	N	CA	C
 HC 1.008	0.31	-1

; added by Justin Lemkul 
[ 5TER ]
[ replace ]
 O5'	ON5  15.9994 -0.66
 C5'	CN8B 12.011   0.05
[ add ]
 1	2  H5T	O5'  C5'  C4'
	HN5  1.008	0.43	-1
[ delete ]
 P
 O1P
 O2P