Where can I find atomic coordinates for guanosine / cytosine / thymine / adenine (either the ribonucleotide or deoxyribonucleotide bases) where the atoms are configured in the manner we would expect in the context of an idealized B-form or A-form nucleic acid duplex? I'd like to calculate the angle between various bonds in these bases, and to play around with a few other things, but I'm having trouble finding proper atomic coordinate sets.
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$\begingroup$ I have no idea about this, but I found something you might want to check out: onlinelibrary.wiley.com/doi/10.1046/j.1432-1327.1999.00270.x/… If it has no supporting information you might find structures at ccdc.cam.ac.uk $\endgroup$– Martin - マーチン ♦Commented Jul 31, 2014 at 15:47
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2 Answers
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I played around with a program called GROMACS about 4 years ago and don't remember much, but I do remember doing a tutorial simulating a DNA double helix and part of it included making the DNA by giving it a sequence and running a script. It can probably make A or B form.
EDIT: This was a long time ago and I forgot. It wasn't GROMACS, it was Amber. Look here http://ambermd.org/tutorials/ Tutorial B1 looks like the same tutorial I did with the DNA.
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In Protein Data Bank (RCBS), for example as molecule of the months: http://www.rcsb.org/pdb/101/motm.do?momID=23&evtc=Suggest&evta=Moleculeof%20the%20Month&evtl=OtherOptions
In Nuclear Acid Database: http://ndbserver.rutgers.edu/
