Dear all,
I am simulating DNA duplexes with intercalating hydrophobic, charged small molecules/dyes. I wonder which of the force fields is considered to be the best to date to provide the most reliable conformations for a DNA duplex? I am particularly interested in the conformations of the sugars.
I have this question because I have performed a couple of 10ns runs with ff99 and ff10 parameters of just DNA duplex of 16 bp long to examine the performance of the force fields. The setup of the test runs is very simple, unrestrained MD in NTP ensemble, explicit solvent (TIP3P), neutralized system with Na+.
Both ff sets performed reasonably good, the average structures do still look like B-form DNAs. Though, I have noticed some problems with the performance. When ff99is used the DNA becomes extended with time, the problem that was corrected in ff10. On the other hand, the ff10 force fields set provides smaller rise (bp to bp distance) of 2.8Å, while the ff99 gives the expected value of 3.36Å. ff99 also introduces bp inclination after some time, which is not the case with ff10. However, neither ff99 nor ff10 provides reasonable sugar puckers values... Though the ff99 set gives much more stable values for the sugar pucker then ff10, which just covers all possible conformations. This is just DNA, and when I introduce any of my dyes, the values for sugars are all over the conformation space with both ff sets.
The knowledge about the sugar conformations is crucial for me, since from the experimental data the transition to A-form DNA is suspected, and it would have been nice to observe it with the MD. There is no crystal/nmr structures to use as a starting/reference point. So any ideas/suggestions would be very appreciated!
Best regards,
Anna
-----------
Anna Reymer,
Physical Chemistry,
Department of Chemical and Biological Engineering
Chalmers University of Technology
Kemivägen 10
SE-412 96 Gothenburg
Sweden
Phone: +46-(0)31-7722815
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Received on Thu Jun 02 2011 - 07:30:04 PDT
