Singh wrote:
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 !!
Both the .rtp and .hdb entries specify that an H5T atom should be present (.rtp)
or otherwise added (.hdb). If this is not what you want, then don't tell
pdb2gmx to build it. Note that you'll have to re-parameterize the molecule
since you'll be changing the charge state by deprotonating this group.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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