Singh wrote:
Hi all,
As per Justin's suggestion , I have created a rtp entry for primed THY
residue..which is like this ..
[ DT5P ]
[ 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
O3P O2 -0.77610 34
[ bonds ]
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
and the THY with terminal Phosphate group is...
ATOM 1 O5' DT A 1 -5.444 -3.882 -27.274 1.00 0.00 O
ATOM 2 C5' DT A 1 -4.975 -5.193 -26.943 1.00 0.00 C
ATOM 3 1H5' DT A 1 -4.594 -5.667 -27.848 1.00 0.00 H
ATOM 4 2H5' DT A 1 -5.809 -5.781 -26.560 1.00 0.00 H
ATOM 5 C4' DT A 1 -3.861 -5.152 -25.898 1.00 0.00 C
ATOM 6 H4' DT A 1 -3.531 -6.170 -25.685 1.00 0.00 H
ATOM 7 O4' DT A 1 -2.738 -4.387 -26.383 1.00 0.00 O
ATOM 8 C1' DT A 1 -2.272 -3.512 -25.342 1.00 0.00 C
ATOM 9 H1' DT A 1 -1.204 -3.694 -25.215 1.00 0.00 H
ATOM 10 N1 DT A 1 -2.478 -2.073 -25.683 1.00 0.00 N
ATOM 11 C6 DT A 1 -3.733 -1.556 -25.872 1.00 0.00 C
ATOM 12 H6 DT A 1 -4.556 -2.210 -26.150 1.00 0.00 H
ATOM 13 C2 DT A 1 -1.358 -1.256 -25.798 1.00 0.00 C
ATOM 14 O2 DT A 1 -0.205 -1.685 -25.775 1.00 0.00 O
ATOM 15 N3 DT A 1 -1.613 0.096 -25.966 1.00 0.00 N
ATOM 16 H3 DT A 1 -0.819 0.705 -26.089 1.00 0.00 H
ATOM 17 C4 DT A 1 -2.857 0.699 -25.989 1.00 0.00 C
ATOM 18 O4 DT A 1 -2.954 1.918 -26.111 1.00 0.00 O
ATOM 19 C5 DT A 1 -3.955 -0.231 -25.855 1.00 0.00 C
ATOM 20 C7 DT A 1 -5.368 0.283 -25.580 1.00 0.00 C
ATOM 21 H71 DT A 1 -5.381 1.373 -25.594 1.00 0.00 H
ATOM 22 H72 DT A 1 -5.685 -0.067 -24.597 1.00 0.00 H
ATOM 23 H73 DT A 1 -6.051 -0.098 -26.340 1.00 0.00 H
ATOM 24 C2' DT A 1 -2.985 -4.008 -24.085 1.00 0.00 C
ATOM 25 2H2' DT A 1 -2.460 -4.883 -23.698 1.00 0.00 H
ATOM 26 1H2' DT A 1 -3.043 -3.243 -23.310 1.00 0.00 H
ATOM 27 C3' DT A 1 -4.324 -4.508 -24.586 1.00 0.00 C
ATOM 28 H3' DT A 1 -4.981 -3.657 -24.744 1.00 0.00 H
ATOM 29 O3' DT A 1 -4.947 -5.483 -23.741 1.00 0.00 O
ATOM 30 P DT A 1 -6.751 -3.677 -28.479 1.00 0.00 P
ATOM 31 O1P DT A 1 -7.056 -2.218 -28.645 1.00 0.00 O
ATOM 32 O2P DT A 1 -7.982 -4.394 -28.010 1.00 0.00 O1-
ATOM 33 O3P DT A 1 -6.283 -4.285 -29.883 1.00 0.00 O
...it started creating top and Gro files but.. when I checked visually by VMD i
found that in Gro file an H is placed between CH2O and PHOSPHATE group while in
my pdb it's a proper terminal... like , -CH2O-PO3..?
Can anyone suggest me any further changes I am supposed to made in these files !
I don't see how this worked in the first place. You've defined a residue named
"DT5P" but then expect that to be mapped onto "DT" (which it should not). Are
you reconstructing H positions via an .hdb entry as well? I suspect you have to
be, due to the absence of H5T, which is in the .rtp entry but not the .pdb
coordinates. If an H atom is being placed strangely, then probably you've not
assigned the correct geometry in the .hdb entry. See the manual.
-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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