[gmx-users] GMX-compatible DNA coordinates

[Alex]

Mauricio,

That is very useful, thanks a lot. I'll try it in a bit.

Alex


MEN> Alex,


MEN> You can use X3DNA to produce any nucleic acid geometry you’d like and
MEN> gromacs pdb2gmx will understand it.

MEN> For example, to create a single-strand of 16 DNA bases you only need a file
MEN> with the corresponding rigid-body base-step parameters such as the
MEN> ssdna.par file shown below:

MEN>   16 # bases
MEN>    0 # ***local step parameters***
MEN> #      Shift     Slide     Rise      Tilt      Roll      Twist
MEN> T      0.000     0.000     0.000     0.000     0.000     0.000
MEN> A      0.280    -0.664     3.201     2.499    -2.895    32.486
MEN> C     -0.314    -0.644     2.640     8.643     2.631    28.956
MEN> C      0.424    -0.849     3.240     1.756     1.690    33.400
MEN> A      1.519    -0.396     3.077     4.184     6.152    39.140
MEN> A      0.412    -0.670     2.797     6.577    11.309    26.608
MEN> C     -0.183    -2.185     2.859     6.133     5.126    17.125
MEN> A      0.423    -1.477     6.195   -18.545   -26.691    36.074
MEN> C      1.216    -0.879     3.063     5.417     8.466    35.858
MEN> A     -9.111    -4.794    -5.433    74.829    43.216   -56.814
MEN> C      3.440     0.344     3.176     3.036    12.621    42.046
MEN> A     -9.111    -4.794    -5.433    74.829    43.216   -56.814
MEN> C      3.440     0.344     3.176     3.036    12.621    42.046
MEN> A      1.478     0.681     3.056    13.088     0.208    44.226
MEN> A     -0.358    -0.777     3.494    -2.803    -4.534    33.162
MEN> A     -0.264    -0.272     2.833     9.637     1.457    30.508



MEN> With such a file at hand all you have to do is issue the following two
MEN> commands to 3DNA.

MEN>     x3dna_utils cp_std -d BDNA

MEN> Which copies a standard BDNA backbone scaffold in the folder you’re at, and
MEN> then:

MEN>     rebuild -atomic ssdna.par ssdna.pdb

MEN> This will generate the file ssdna.pdb which you can find at:

MEN> http://wikisend.com/download/614970/ssdna.pdb

MEN> It works with:

MEN>     pdb2gmx -f ssdna.pdb -o start.pdb -p topol.top -i posre.itp -ff
MEN> charmm27 -water tip3p

MEN> In principle the online version of 3DNA, w3dna, would also work for
MEN> generating nucleic acid models of any desired sequence. But sadly the X3DNA
MEN> version working in the backend of the webserver is awfully outdated and
MEN> uses the old convention of simply A, G, T, C, instead of DA, DG, DT, DC, to
MEN> name the nucleotide residues.


MEN> Hope this helps,


MEN> Mauricio



MEN> +++++++++++++++++++++++++++++++++++++++++++++++
MEN>  Mauricio Esguerra Neira, Ph.D.
MEN>  Post-Doctoral Fellow
MEN>  Hugo Gutiérrez de Terán P.I.
MEN>  Department of Cell and Molecular Biology
MEN>  Uppsala University
MEN>  Phone Number: (+46)073-678-5334
MEN>  mesguerra.org
MEN>  mauricio.esguerra at icm.uu.se
MEN> +++++++++++++++++++++++++++++++++++++++++++++++