Hi Friends,
could anyone please guide me to get rid of the 5' H atom in terminal DT
nucleotide. These are my entries..
PDB : 5'DT
ATOM 1 P DT A 1 -6.726 -4.074 -28.509 1.00 0.00 P
ATOM 2 O5' DT A 1 -5.444 -3.882 -27.274 1.00 0.00 O1-
ATOM 3 C5' DT A 1 -4.975 -5.193 -26.943 1.00 0.00 C
ATOM 4 1H5' DT A 1 -4.594 -5.667 -27.848 1.00 0.00 H
ATOM 5 2H5' DT A 1 -5.809 -5.781 -26.560 1.00 0.00 H
ATOM 6 C4' DT A 1 -3.861 -5.152 -25.898 1.00 0.00 C
ATOM 7 H4' DT A 1 -3.531 -6.170 -25.685 1.00 0.00 H
ATOM 8 O4' DT A 1 -2.738 -4.387 -26.383 1.00 0.00 O
ATOM 9 C1' DT A 1 -2.272 -3.512 -25.342 1.00 0.00 C
ATOM 10 H1' DT A 1 -1.204 -3.694 -25.215 1.00 0.00 H
ATOM 11 N1 DT A 1 -2.478 -2.073 -25.683 1.00 0.00 N
ATOM 12 C6 DT A 1 -3.733 -1.556 -25.872 1.00 0.00 C
ATOM 13 H6 DT A 1 -4.556 -2.210 -26.150 1.00 0.00 H
ATOM 14 C2 DT A 1 -1.358 -1.256 -25.798 1.00 0.00 C
ATOM 15 O2 DT A 1 -0.205 -1.685 -25.775 1.00 0.00 O
ATOM 16 N3 DT A 1 -1.613 0.096 -25.966 1.00 0.00 N
ATOM 17 H3 DT A 1 -0.819 0.705 -26.089 1.00 0.00 H
ATOM 18 C4 DT A 1 -2.857 0.699 -25.989 1.00 0.00 C
ATOM 19 O4 DT A 1 -2.954 1.918 -26.111 1.00 0.00 O
ATOM 20 C5 DT A 1 -3.955 -0.231 -25.855 1.00 0.00 C
ATOM 21 C7 DT A 1 -5.368 0.283 -25.580 1.00 0.00 C
ATOM 22 H71 DT A 1 -5.381 1.373 -25.594 1.00 0.00 H
ATOM 23 H72 DT A 1 -5.685 -0.067 -24.597 1.00 0.00 H
ATOM 24 H73 DT A 1 -6.051 -0.098 -26.340 1.00 0.00 H
ATOM 25 C2' DT A 1 -2.985 -4.008 -24.085 1.00 0.00 C
ATOM 26 1H2' DT A 1 -2.460 -4.883 -23.698 1.00 0.00 H
ATOM 27 2H2' DT A 1 -3.043 -3.243 -23.310 1.00 0.00 H
ATOM 28 C3' DT A 1 -4.324 -4.508 -24.586 1.00 0.00 C
ATOM 29 H3' DT A 1 -4.981 -3.657 -24.744 1.00 0.00 H
ATOM 30 O3' DT A 1 -4.947 -5.483 -23.741 1.00 0.00 O
ATOM 31 O1P DT A 1 -7.256 -2.725 -28.895 1.00 0.00
O1-
ATOM 32 O2P DT A 1 -7.840 -4.907 -27.948 1.00 0.00 O1-
RTP Entry : DT5
[ DT5 ]
[ atoms ]
H5T HO 0.44220 1
O5' O -0.63180 2
C5' CT -0.00690 3
H5'1 H1 0.07540 4
H5'2 H1 0.07540 5
C4' CT 0.16290 6
H4' H1 0.11760 7
O4' OS -0.36910 8
C1' CT 0.06800 9
H1' H2 0.18040 10
N1 N* -0.02390 11
C6 CM -0.22090 12
H6 H4 0.26070 13
C5 CM 0.00250 14
C7 CT -0.22690 15
H71 HC 0.07700 16
H72 HC 0.07700 17
H73 HC 0.07700 18
C4 C 0.51940 19
O4 O -0.55630 20
N3 NA -0.43400 21
H3 H 0.34200 22
C2 C 0.56770 23
O2 O -0.58810 24
C3' CT 0.07130 25
H3' H1 0.09850 26
C2' CT -0.08540 27
H2'1 HC 0.07180 28
H2'2 HC 0.07180 29
O3' OS -0.52320 30
P P 1.16590 31
O1P O2 -0.77610 32
O2P O2 -0.77610 33
[ bonds ]
O1P P
O2P P
O3P H5T
O5' P
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 C7
C5 C4
C7 H71
C7 H72
C7 H73
C4 O4
C4 N3
N3 H3
N3 C2
C2 O2
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
[ impropers ]
C2 C6 N1 C1'
C4 C6 C5 C7
N1 N3 C2 O2
C5 N3 C4 O4
C4 C2 N3 H3
N1 C5 C6 H6
HDB Entry for DT5 (modified)
DT5 9
1 2 H5T O2P P O5'
2 6 H5' C5' O5' C4'
1 5 H4' C4' C5' O4' C3'
1 5 H1' C1' O4' N1 C2'
1 1 H6 C6 N1 C5
3 4 H7 C7 C5 C6
1 1 H3 N3 C4 C2
1 5 H3' C3' C4' C2' O3'
2 6 H2' C2' C1' C3'
I am trying a lot to solve this problem .. but Unfortunately I am not able.. :(
.. Please have a look and if possible make some suggestions on RTP or HDB
entry !!
Raghav
Research Scholar
IEMN, University of Science and Technology
Villeneuve d'ascq, Lille, France
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