more test.ptraj
trajin dna_solv_md1.mdcrd 1 599 100
strip :WAT,Na+
center :1-12 mass origin
image origin center familiar
trajout output.pdb pdb append
ptraj dna_solv.top < test.ptraj
2) rodar o find_pair
find_pair [OPTION] PDBFILE OUTFILE
3)
ANÁLISE PARA UM FRAME:
analyse dna.inp
ANÁLISE PARA UMA TRAJETÓRIA:
rodar o x3dna_ensemble analyze -b dna.inp -e output.pdb
/Desktop/DNA/DNA_6/GCCGGC/4-MD
ASSIM COM O INPUT (dna.inp), executar o comando analyse:
analyse dna.inp
EXECUTA O COMANDO:
find_pair dna.pdb dna.inp
handling file
uncommon residue DG5 1 on chain [#1] assigned to: g
uncommon residue DC3 6 on chain [#6] assigned to: c
uncommon residue DG5 7 on chain [#7] assigned to: g
uncommon residue DC3 12 on chain [#12] assigned to: c
Assim obtém o arquivo de input dna.inp
dna.pdb
dna.out
2 # duplex
6 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 12 0 # 1 | ..1.>-:...1_:[DG5]g-----c[DC3]:..12_:-<..1. 0.21 0.16 32.59 8.95 -2.84
2 11 0 # 2 | ..1.>-:...2_:[.DC]C-----G[.DG]:..11_:-<..1. 1.29 1.27 22.18 9.05 -0.06
3 10 0 # 3 | ..1.>-:...3_:[.DG]G-----C[.DC]:..10_:-<..1. 0.95 0.82 18.09 9.13 -1.51
4 9 0 # 4 | ..1.>-:...4_:[.DC]C-----G[.DG]:...9_:-<..1. 0.93 0.22 14.21 8.93 -2.92
5 8 0 # 5 | ..1.>-:...5_:[.DG]G-----C[.DC]:...8_:-<..1. 0.58 0.48 23.29 9.03 -2.28
6 7 0 # 6 | ..1.>-:...6_:[DC3]c-----g[DG5]:...7_:-<..1. 1.62 1.61 36.71 8.63 1.67
##### Base-pair criteria used: 4.00 0.00 15.00 2.50 65.00 4.50 7.80 [ O N]
##### 0 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (6): 1 - 6
3) rodar o x3dna_ensemble analyze -b dna.inp -e output.pdb
/Desktop/DNA/DNA_6/GCCGGC/4-MD
ASSIM COM O INPUT (dna.inp), executar o comando analyse:
analyse dna.inp
more dna.out
****************************************************************************
3DNA v2.1 (2013), created and maintained by Xiang-Jun Lu (PhD)
****************************************************************************
1. The list of the parameters given below correspond to the 5' to 3' direction
of strand I and 3' to 5' direction of strand II.
2. All angular parameters, except for the phase angle of sugar pseudo-
rotation, are measured in degrees in the range of [-180, +180], and all
displacements are measured in Angstrom units.
****************************************************************************
File name: dna.pdb
Date and time: Thu Oct 10 15:18:44 2013
Number of base-pairs: 6
Number of atoms: 386
****************************************************************************
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)
Strand I Strand II Helix
1 (0.068) ..1.>-:...1_:[DG5]g-----c[DC3]:..12_:-<..1. (0.035) |
2 (0.032) ..1.>-:...2_:[.DC]C-----G[.DG]:..11_:-<..1. (0.069) |
3 (0.058) ..1.>-:...3_:[.DG]G-----C[.DC]:..10_:-<..1. (0.038) |
4 (0.033) ..1.>-:...4_:[.DC]C-----G[.DG]:...9_:-<..1. (0.063) |
5 (0.049) ..1.>-:...5_:[.DG]G-----C[.DC]:...8_:-<..1. (0.049) |
6 (0.030) ..1.>-:...6_:[DC3]c-----g[DG5]:...7_:-<..1. (0.057) |
****************************************************************************
(RMSD em relação ao DNA canônico)
****************************************************************************
Detailed H-bond information: atom-name pair and length [ O N]
1 g-----c [3] O6 - N4 3.02 N1 - N3 2.81 N2 - O2 3.01
2 C-----G [3] N4 - O6 3.39 N3 - N1 3.02 O2 - N2 2.92
3 G-----C [3] O6 - N4 3.48 N1 - N3 3.14 N2 - O2 2.74
4 C-----G [3] N4 - O6 2.93 N3 - N1 2.99 O2 - N2 2.98
5 G-----C [3] O6 - N4 3.10 N1 - N3 3.06 N2 - O2 2.98
6 c-----g [3] N4 - O6 2.98 N3 - N1 2.93 O2 - N2 2.78
****************************************************************************
(distância das ligações de hidrogênio entre as bases)
****************************************************************************
Overlap area in Angstrom^2 between polygons defined by atoms on successive
bases. Polygons projected in the mean plane of the designed base-pair step.
Values in parentheses measure the overlap of base ring atoms only. Those
outside parentheses include exocyclic atoms on the ring. Intra- and
inter-strand overlap is designated according to the following diagram:
i2 3' 5' j2
/|\ |
| |
Strand I | | II
| |
| |
| \|/
i1 5' 3' j1
step i1-i2 i1-j2 j1-i2 j1-j2 sum
1 gC/Gc 0.86( 0.04) 0.00( 0.00) 0.00( 0.00) 1.65( 0.35) 2.52( 0.39)
2 CG/CG 0.60( 0.00) 0.00( 0.00) 0.55( 0.00) 2.97( 0.80) 4.13( 0.80)
3 GC/GC 3.83( 1.49) 0.00( 0.00) 0.00( 0.00) 5.22( 2.35) 9.05( 3.84)
4 CG/CG 1.21( 0.00) 0.00( 0.00) 1.12( 0.00) 0.58( 0.00) 2.90( 0.00)
5 Gc/gC 4.67( 2.05) 0.00( 0.00) 0.00( 0.00) 2.43( 0.37) 7.11( 2.43)
****************************************************************************
(valores mais importantes são os entre parênteses)
The same strand (intrastrand crosslink) The opposite strands of the DNA (interstrand crosslink).
****************************************************************************
Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in
the coordinate system of the given structure
bp Ox Oy Oz Nx Ny Nz
1 g-c 29.711 27.758 19.769 -0.256 -0.075 0.964
2 C-G 29.755 27.143 24.577 0.214 0.006 0.977
3 G-C 30.188 27.559 27.233 0.125 0.062 0.990
4 C-G 30.319 28.629 31.019 0.126 0.179 0.976
5 G-C 30.297 28.839 34.366 0.066 0.172 0.983
6 c-g 30.555 29.126 38.647 -0.095 0.297 0.950
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 g-c -0.01 -0.13 0.16 15.10 28.88 -0.04
2 C-G 0.19 -0.17 1.27 -11.34 -19.07 -3.46
3 G-C -0.40 0.27 0.82 13.24 -12.34 9.70
4 C-G 0.85 -0.31 0.22 -8.56 -11.34 -4.12
5 G-C 0.33 0.00 0.48 -14.21 -18.45 -2.44
6 c-g -0.08 -0.10 1.61 -36.36 5.08 3.49
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.15 -0.07 0.76 -7.02 -4.54 0.52
s.d. 0.43 0.20 0.59 19.15 18.55 5.28
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 gC/Gc -0.00 0.47 4.82 -4.10 -27.28 42.72
2 CG/CG -0.25 -0.21 2.70 6.04 0.54 26.19
3 GC/GC -0.60 -0.36 3.87 -0.07 -6.79 46.04
4 CG/CG 0.07 -0.51 3.31 2.96 -1.85 33.13
5 Gc/gC 0.47 -0.64 4.22 -5.17 -10.62 40.75
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.06 -0.25 3.79 -0.07 -9.20 37.77
s.d. 0.40 0.43 0.82 4.71 11.00 8.02
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 gC/Gc 3.38 -0.42 3.88 -33.60 5.05 50.50
2 CG/CG -0.57 1.80 2.58 1.17 -13.11 26.87
3 GC/GC 0.23 0.76 3.89 -8.62 0.09 46.51
4 CG/CG -0.57 0.37 3.33 -3.23 -5.17 33.31
5 Gc/gC 0.53 -1.35 4.17 -14.88 7.25 42.36
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.60 0.23 3.57 -11.83 -1.18 39.91
s.d. 1.63 1.19 0.63 13.57 8.21 9.68
****************************************************************************
Structure classification:
This is a right-handed nucleic acid structure
****************************************************************************
lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the
base-pair C1'-C1' line
C1'-C1': distance between C1' atoms for each base-pair
RN9-YN1: distance between RN9-YN1 atoms for each base-pair
RC8-YC6: distance between RC8-YC6 atoms for each base-pair
bp lambda(I) lambda(II) C1'-C1' RN9-YN1 RC8-YC6
1 g-c 58.2 50.6 10.7 8.9 9.8
2 C-G 56.2 50.9 10.8 9.0 9.9
3 G-C 58.1 62.1 10.6 9.1 10.3
4 C-G 58.7 45.6 10.8 8.9 9.7
5 G-C 56.3 47.6 10.9 9.0 10.0
6 c-g 55.2 54.8 10.3 8.6 9.6
****************************************************************************
Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases
step Xp Yp Zp XpH YpH ZpH Form
1 gC/Gc -2.14 8.79 0.78 0.93 7.93 -3.88
2 CG/CG -2.90 9.00 0.75 -3.64 8.98 1.13
3 GC/GC -3.15 8.91 -0.17 -2.94 8.80 -1.40 B
4 CG/CG -2.62 9.28 0.30 -3.09 9.29 -0.16 B
5 Gc/gC -2.90 8.45 0.49 -2.57 8.33 -1.52 B
****************************************************************************
Minor and major groove widths: direct P-P distances and refined P-P distances
which take into account the directions of the sugar-phosphate backbones
(Subtract 5.8 Angstrom from the values to take account of the vdw radii
of the phosphate groups, and for comparison with FreeHelix and Curves.)
Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.
Minor Groove Major Groove
P-P Refined P-P Refined
1 gC/Gc --- --- --- ---
2 CG/CG --- --- --- ---
3 GC/GC 9.3 --- 15.7 ---
4 CG/CG --- --- --- ---
5 Gc/gC --- --- --- ---
****************************************************************************
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.24(0.42)
Helix: 0.050 0.095 0.994
HETATM 9998 XS X X 999 30.158 27.323 21.130
HETATM 9999 XE X X 999 30.960 28.830 36.932
Average and standard deviation of helix radius:
P: 9.32(0.43), O4': 6.32(0.50), C1': 5.83(0.36)
Global parameters based on C1'-C1' vectors:
disp.: displacement of the middle C1'-C1' point from the helix
angle: inclination between C1'-C1' vector and helix (subtracted from 90)
twist: helical twist angle between consecutive C1'-C1' vectors
rise: helical rise by projection of the vector connecting consecutive
C1'-C1' middle points onto the helical axis
bp disp. angle twist rise
1 g-c 1.81 -4.90 43.18 2.80
2 C-G 1.54 -6.45 30.09 3.81
3 G-C 2.48 -5.11 39.24 2.89
4 C-G 2.74 -9.14 35.00 2.93
5 G-C 2.86 -7.24 44.91 3.46
6 c-g 2.93 -4.36 --- ---
****************************************************************************
Main chain and chi torsion angles:
Note: alpha: O3'(i-1)-P-O5'-C5'
beta: P-O5'-C5'-C4'
gamma: O5'-C5'-C4'-C3'
delta: C5'-C4'-C3'-O3'
epsilon: C4'-C3'-O3'-P(i+1)
zeta: C3'-O3'-P(i+1)-O5'(i+1)
chi for pyrimidines(Y): O4'-C1'-N1-C2
chi for purines(R): O4'-C1'-N9-C4
Strand I
base alpha beta gamma delta epsilon zeta chi
1 g --- --- 72.5 144.7 -85.0 120.4 -63.7
2 C -93.5 126.6 63.4 82.9 170.0 -68.6 -152.4
3 G -67.9 177.4 74.5 152.4 -172.8 -103.8 -110.2
4 C -68.7 176.8 43.5 116.9 174.4 -92.7 -131.0
5 G -59.6 159.0 72.7 138.1 175.1 -88.7 -131.0
6 c -88.1 -138.7 48.9 150.9 --- --- -120.8
Strand II
base alpha beta gamma delta epsilon zeta chi
1 c -59.8 147.8 52.4 140.8 --- --- -123.5
2 G -59.3 160.5 48.7 134.5 -134.0 177.8 -95.1
3 C -75.3 -153.5 52.5 132.5 -167.6 -90.7 -110.2
4 G -56.4 170.9 51.4 131.3 170.5 -84.6 -121.8
5 C -74.2 179.4 59.8 134.6 175.6 -93.0 -110.6
6 g --- --- 48.4 152.4 -162.9 -126.8 -108.0
****************************************************************************
****************************************************************************
Sugar conformational parameters:
Note: v0: C4'-O4'-C1'-C2'
v1: O4'-C1'-C2'-C3'
v2: C1'-C2'-C3'-C4'
v3: C2'-C3'-C4'-O4'
v4: C3'-C4'-O4'-C1'
tm: the amplitude of pucker
P: the phase angle of pseudorotation
Strand I
base v0 v1 v2 v3 v4 tm P Puckering
1 g -28.1 41.9 -37.6 25.0 0.9 40.5 158.4 C2'-endo
2 C -9.9 -8.4 21.4 -28.9 24.9 27.9 40.1 C4'-exo
3 G -16.7 35.1 -38.7 29.5 -8.0 39.0 173.2 C2'-endo
4 C -29.9 25.5 -12.1 -5.2 23.7 30.0 113.7 C1'-exo
5 G -40.8 46.8 -36.5 12.8 17.1 47.2 140.7 C1'-exo
6 c -15.5 29.9 -31.3 23.3 -4.9 31.8 169.9 C2'-endo
Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 c -12.0 26.3 -29.8 24.2 -8.4 29.9 176.4 C2'-endo
2 G -40.2 49.2 -32.9 12.7 15.4 44.5 137.7 C1'-exo
3 C -7.8 22.9 -27.2 21.7 -8.8 27.2 179.9 C2'-endo
4 G -35.9 46.0 -37.2 17.8 10.4 44.4 146.9 C2'-endo
5 C -23.5 32.8 -30.1 15.8 4.9 33.5 153.8 C2'-endo
6 g -15.5 27.9 -28.8 22.4 -4.8 29.3 169.7 C2'-endo
****************************************************************************
****************************************************************************
Same strand P--P and C1'--C1' virtual bond distances
Strand I Strand II
step P--P C1'--C1' step P--P C1'--C1'
1 g/C --- 4.48 1 c/G 6.67 5.37
2 C/G 6.79 5.46 2 G/C 6.55 4.19
3 G/C 7.46 4.93 3 C/G 7.10 5.30
4 C/G 6.76 4.62 4 G/C 7.08 4.64
5 G/c 7.41 5.85 5 C/g --- 5.50
****************************************************************************
Helix radius (radial displacement of P, O4', and C1' atoms in local helix
frame of each dimer)
Strand I Strand II
step P O4' C1' P O4' C1'
1 gC/Gc 7.86 4.28 4.44 8.11 4.98 5.17
2 CG/CG 10.76 8.64 7.85 8.80 5.33 4.68
3 GC/GC 10.15 7.01 6.43 8.42 5.44 5.10
4 CG/CG 9.95 6.71 6.12 9.64 6.61 6.00
5 Gc/gC 7.17 4.36 4.04 10.35 7.71 7.12
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step
step Px Py Pz Hx Hy Hz
1 gC/Gc 32.76 28.04 22.22 -0.11 0.48 0.87
2 CG/CG 28.25 27.96 26.09 0.05 -0.16 0.99
3 GC/GC 29.56 28.30 29.09 -0.01 0.12 0.99
4 CG/CG 30.38 28.09 32.73 0.11 0.08 0.99
5 Gc/gC 30.20 30.31 36.43 -0.18 0.02 0.98
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