95 lines
3.6 KiB
Plaintext
95 lines
3.6 KiB
Plaintext
This directory contains example data and input files
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as well as utility scripts for the oxDNA/oxDNA2/oxRNA2
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coarse-grained model of DNA and RNA.
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/******************************************************************************/
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/examples/oxDNA/duplex1:
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/examples/oxDNA2/duplex1:
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Input, data and log files for a DNA duplex (double-stranded DNA)
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consisiting of 5 base pairs. The duplex contains two strands with
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complementary base pairs. The topology is
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A - C - G - T - A
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T - G - C - A - T
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Note that in this example the stacking and hydrogen-bonding interactions
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are sequence-averaged (cf. keyword 'seqav' in according pair styles).
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/******************************************************************************/
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/examples/oxDNA/duplex2:
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/examples/oxDNA2/duplex2:
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Input, data and log files for a nicked DNA duplex (double-stranded DNA)
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consisiting of 8 base pairs. The duplex contains strands with
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complementary base pairs, but the backbone on one side is not continuous:
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two individual strands on one side form a duplex with a longer single
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strand on the other side. The topology is
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A - C - G - T - A - C - G - T
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T - G - C - A T - G - C - A
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Note that in this example the stacking and hydrogen-bonding interactions
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are sequence-averaged (cf. keyword 'seqav' in according pair styles).
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/******************************************************************************/
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/examples/oxDNA2/duplex3:
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This example uses the duplex1 with sequence-dependent stacking and
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hydrogen-bonding interactions and both nucleotide mass and
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moment of inertia set to the value used in the standalone implementation
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of oxDNA (M = I = 1). The masses can be set directly in the input and
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data file, whereas the moment of inertia is set via the diameter of the
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ellipsoid in the data file and has a value of 3.16227766.
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The change of mass and moment of inertia allows direct comparison of
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trajectory data or time-dependent observables on a per-timestep basis.
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As mentioned above, the stacking and hydrogen-bonding interactions
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are sequence-dependent (cf. keyword 'seqdep' in according pair styles).
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/******************************************************************************/
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/examples/oxDNA2/unique_bp:
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This example uses atom types 1-8 to model a 13 base pair duplex.
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The nucleotide types are assigned as follows:
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A = 1,5; C = 2,6; G = 3,7; T = 4,8
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The topology is
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A C G T A C G T A C G T A
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1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 1 - 2 - 7 - 8 - 1
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4 - 3 - 2 - 1 - 8 - 7 - 6 - 5 - 4 - 3 - 6 - 5 - 4
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T G C A T G C A T G C A T
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With a large (32 or 64) number of atom types quasi-unique base pairing
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between two individual nucleotides can be established.
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/******************************************************************************/
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/examples/oxDNA2/dsring:
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This example uses a dsDNA ring of 74 base pairs. The bonds which close the ring
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are (in 3' to 5' direction) between nucleotide 74 and 1 and between nucleotide
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148 and 75, respectively.
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/******************************************************************************/
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/examples/oxRNA2/duplex2
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This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or
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oxDNA2 force field. Sequence-dependent stacking and hydrogen-bonding
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strengths enabled (cf. keyword 'seqdep' in according pair styles).
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/******************************************************************************/
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/util:
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This directory contains a simple python setup tool which creates
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single straight or helical DNA strands, DNA duplexes or arrays of DNA
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duplexes.
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