Computational Chemistry: outubro 2013

terça-feira, 1 de outubro de 2013

Amber frcmod file - Dihedral info

Here I show the dihedral part of the frcmod file from Amber code.

DIHE divider Force Phase Periodicity
ca-ca-cd-cc 1 2.550 180.000 2.000 same as X -c2-ca-X
ca-ca-cd-nh 1 2.550 180.000 2.000 same as X -c2-ca-X
na-cc-os-Cu 1 1.050 180.000 2.000 same as X -c2-os-X (?)
cc-os-Cu-nh 1 1.050 1.000 2.000 ATTN, need revision (?)
cc-os-Cu-os 1 0.000 180.000 2.000 ATTN, need revision (?)
cd-cc-os-Cu 1 1.050 180.000 2.000 same as X -c2-os-X (?)
cd-nh-Cu-os 1 1.050 1.000 2.000 ATTN, need revision (?)
cd-nh-Cu-nh 1 1.050 180.000 2.000 ATTN, need revision (?)
os-Cu-nh-c3 1 1.050 178.000 2.000 MBG, need revision
os-Cu-nh-cc 1 1.050 180.000 6.900 MBG, at least 2 minima
os-Cu-os-cd 1 1.050 177.000 2.000 MBG, need revision
Cu-os-cd-cc 1 1.050 0.800 2.000 MBG, as X -c2-os-X
Cu-os-cd-na 1 1.050 179.000 2.000 MBG, same as X -c2-os-X
nh-Cu-nh-c3 1 1.050 2.200 2.000 MBG, need revision
nh-Cu-nh-cc 1 1.050 -176.000 2.000 MBG, need revision
nh-Cu-os-cd 1 1.050 180.000 2.950 MBG, 2 minima
nh-cc-ca-ca 1 2.550 180.000 2.000 same as X -c2-ca-X
cd-cc-ca-ca 1 2.550 180.000 2.000 same as X -c2-ca-X

%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8) (PK(i), i=1,NPTRA)
PK : force constant for the dihedrals of each type, kcal/mol

%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8) (PN(i), i=1,NPTRA)
PN : periodicity of the dihedral of a given type

%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8) (PHASE(i), i=1,NPTRA)
PHASE : phase of the dihedral of a given type, radians

http://www.cryst.bbk.ac.uk/PPS95/course/4_mol_forces/os_torg.html

3DNA

1) rodar ptraj pra converter a trajetória mdcrd em pdb:

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

Não sei o que são os valores a direita

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

prep file

Data from: http://ambermd.org/doc/prep.html

It is not necessary to run PREP if all residues needed for a simulation are already present in the standard AMBER database, described in the LINK documentation.

Dummy atoms: PREP requires that three dummy atoms  precede
the  actual  atoms of the residue.  These atoms are simply used
to define the space axes for  the  residue.   The  three  dummy
atoms  must be given the topological type "M", and they must be
assigned a force field atom type that defines them   as   dummy
atoms.   The   symbol   "DU"   is  recommended to be consistent
with the standard database.   It  is  necessary  to  have   the
three  initial   dummy   atoms   whether  internal or cartesian
coordinates are given as input.

A 4° coluna pode ser representada por "Main", "Side", "Branch", "3", "4", "5" "6" e "End" tipos..
Observe que E (end) são os átomos que possui apenas uma ligação, como neste caso são os átomos de hidrogênio.

Autodock

Autodock

Autodock put zero total charge to Cuisaepy. So, the ligand has zro charge and Cu ion has zero charge. I changed by hand the charge of Cu as +1.
The initial docking position was in minor groove with Cu poiting to DNA

The docking results shows an inverted Cuisaepy position with Cu pointing to the outside of the DNA. This because the Cu is highly charged in comparision to the rest of the ligand. So I'll include the resp charges

1) check pdb for DNA+metal-complex
I didn't find it

2) Run resp charges using gaussian

3) Run intercalating complex

/mgltools_x86_64Linux2_1.5.6/bin/pythonsh /mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r DNA.mol2 -C -U lps -o DNAwh.pdbqt

#/mgltools_x86_64Linux2_1.5.6/bin/pythonsh /mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r DNA.mol2 -C -U lps -o DNAwh.pdbqt

/mgltools_x86_64Linux2_1.5.6/bin/pythonsh /mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py -l cie.mol2 -C -p Cu -U lps -o CIEwh.pdbqt

vina --config conf_isaepy.txt --log vina.log

CPMD

mpirun -np 8 cpmd.x cpmd.inp /local/GRS/PROGRAMS_ARCHIVE/CPMD/PP > cpmd.out &

mpdboot -r ssh --totalnumber=4
mpdtrace
mpirun -r ssh -np 24 cpmd.x heating.inp /local/GRS/PROGRAMS_ARCHIVE/CPMD/PP > heating.out &

load WAVEFUNCTION.152.cube; isosurface posname 0.05
"WAVEFUNCTION.152.cube"; isosurface negname -0.05
"WAVEFUNCTION.152.cube"

cpmd2cube.x -halfmesh -psi WAVEFUNCTION.*

Amber iwrap

AMBER MANUAL:
iwrap

If iwrap = 1, the coordinates written to the restart and trajectory files will be "wrapped" into a primary box.

This means that for each molecule, its periodic image closest to the middle of the "primary box" (with x coordinates between 0 and a, y coordinates between 0 and b, and z coordinates between 0 and c) will be the one written to the output file.

This often makes the resulting structures look better visually, but has no effect on the energy or forces.

Performing such wrapping, however, can mess up diffusion and other calculations.

If iwrap = 0, no wrapping will be performed, in which case it is typical to use ptraj as a post-processing program to translate molecules back to the primary box.

For very long runs, setting iwrap = 1 may be required to keep the coordinate output from overflowing the trajectory and restart file formats, especially if trajectories are written in ASCII format instead of NetCDF (see also the ioutfm option). Default = 0.

mpirun -np 8 pmemd.MPI -O -i md6.in -o md6.out -p 3at_solv.top -c 3at_solv_md5.rst -r 3at_solv_md6.rst -x 3at_solv_md6.mdcrd & At this point I changed the input including iwrap=1

Molecule File Format

mol2

http://www.tripos.com/data/support/mol2.pdf

pdb

http://www.wwpdb.org/docs

3DNA commands

$ find_pair
===========================================================================
NAME
find_pair - locate base-pairs and helical regions
SYNOPSIS
find_pair [OPTION] PDBFILE OUTFILE
DESCRIPTION
locate base-pairs and helical regions given a PDB data file. Its
output can be directly fed into analyze, cehs and Lavery's Curves
program.
-s, -1 treat the whole structure as a continuous single helix.
Useful for getting all backbone torsion angles
-c get Curves input for a duplex
-c+ get input for Curves+ (duplex, ATOM records only)
-d generate a separate output file for each helical region
-p find all base-pairs and higher-order base associations
-a read in only the ATOM records, ignoring HETATM records
-z more detailed base-pairing information in the output
-h this help message (any non-recognized options will do)
INPUT
PDB data file
One-letter options can be in either case, any order and combined
EXAMPLES
find_pair sample.pdb sample.inp
find_pair -p sample.pdb allbp_list
find_pair -c+ sample.pdb sample_c+.inp
[then run: Cur+ < sample_c+.inp]
OUTPUT
base-pair listing for input to analyze, cehs and Curves
bestpairs.pdb, hel_regions.pdb, col_chains.scr, col_helices.scr
allpairs.pdb, multiplets.pdb, mulbp.inp
SEE ALSO
analyze, cehs, anyhelix, ex_str, stack2img
AUTHOR
3DNA v2.1 (2013), created and maintained by Xiang-Jun Lu (PhD)

Please post questions/comments on the 3DNA Forum: http://forum.x3dna.org/

x3dna_ensemble extract -h
------------------------------------------------------------------------
Extract 3DNA structural parameters of an ensemble of NMR structures or
MD trajectories, after running 'x3dna_ensemble analyze'. The extracted
parameters are intended to be exported into Excel, Matlab and R etc for
further data analysis/visualization.

Usage:
x3dna_ensemble extract options
Examples:
x3dna_ensemble extract -l
# to see a list of all parameters
x3dna_ensemble extract -p prop
# for propeller, no need to specify full: -p pr suffices
# -p 36 also fine (see above); use 'ensemble_example.out'
x3dna_ensemble extract -p slide -s , -f ensemble_example3.out
# comma separated, from file 'ensemble_example3.out'
x3dna_ensemble extract -p roll -s ' ' -n -o roll.dat
# space separated, no row-label, to file 'roll.dat'
x3dna_ensemble extract -e 1 -p chi1
# extract the chi torsion angle of strand I, but exclude
# those from the two terminal base pairs. For comparison,
# run also: x3dna_ensemble extract -p chi1
x3dna_ensemble extract -a
# extract all parameters, each in a separate file
Options:
------------------------------------------------------------------------
--separator, -s : Separator for fields [\t] (default: )
--par-name, -p : Name of parameter to extract
--fromfile, -f : Parameters file (default: ensemble_example.out)
--outfile, -o : File of selected parameter (default: stdout)
--end-bps, -e : Number of end pairs to ignore (default: 0, 0)
--all, -a: Extract all parameters into separate files
--clean, -c: Clean up parameter files by the -a option
--list, -l: List all parameters
--no-1col, -n: Delete the first (label) column
--help, -h: Show this message

x3dna_ensemble analyze -h

------------------------------------------------------------------------

Analyze a MODEL/ENDMDL delineated ensemble of NMR structures or MD

trajectories. All models must correspond to different conformations

of the same molecule. For the analysis of duplexes (default), a template

base-pair input file, generated with 'find_pair' and manually edited

as necessary, must be provided.

Usage:

x3dna_ensemble analyze options

Examples:

x3dna_ensemble analyze -b bpfile.dat -e sample_md0.pdb

# 21 models (0-20); output (default): 'ensemble_example.out'

# also generate 'model_list.dat', see example below

x3dna_ensemble analyze -b bpfile.dat -m model_list.dat -o ensemble_example2.out

# diff ensemble_example.out ensemble_example2.out

x3dna_ensemble analyze -b bpfile.dat -p 'pdbdir/model_*.pdb' -o ensemble_example3.out

# note to quote the -p option; 20 models (1-20)

# also generate 'pdb_list.dat', see example below

x3dna_ensemble analyze -b bpfile.dat -l pdb_list.dat -o ensemble_example4.out

# diff ensemble_example3.out ensemble_example4.out

# note the order of the models: 1, 10..19, 2, 20, 3..9

x3dna_ensemble analyze -s -e sample_md0.pdb

# perform a 'single'-stranded analysis

x3dna_ensemble analyze -t -e sample_md0.pdb

# calculate all 'torsion' angles

find_pair 355d.pdb 355d.bps

x3dna_ensemble analyze -b 355d.bps --one 355d.pdb

# process the structure file 355d.pdb specified in 355d.bps

Options:

------------------------------------------------------------------------

--bpfile, -b : Name of file containing base-pairing info

--outfile, -o : Output file (default: ensemble_example.out)

--single, -s: Single-stranded DNA/RNA

--torsion, -t: Torsion angles

--ring, -r: Base ring center & normal vector

--ensemble, -e : Ensemble delineated with MODEL/ENDMDL pairs

--models, -m : File containing an explicit list of model numbers

--pattern, -p : Pattern of model files to process (e.g., *.pdb)

--list, -l : File containing an explicit list of models

--one, -n : One regular structure [special case]

--info, -i: Show only model info in the ensemble [with -e]

--help, -h: Show this message

Computational Chemistry

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terça-feira, 1 de outubro de 2013

Amber frcmod file - Dihedral info

3DNA

prep file

Autodock

CPMD

Amber iwrap

mpirun -np 8 pmemd.MPI -O -i md6.in -o md6.out -p 3at_solv.top -c 3at_solv_md5.rst -r 3at_solv_md6.rst -x 3at_solv_md6.mdcrd & At this point I changed the input including iwrap=1

Molecule File Format

3DNA commands

Quem sou eu