[gmx-users] Deformation of DNA duplex

Debayan Chakraborty debayan.ch at gmail.com
Wed Jul 15 21:38:18 CEST 2015

I am not sure if GROMACS can do that type of analysis. But I think 3DNA
should be able to compute the different base pair step parameters.


On Wed, Jul 15, 2015 at 4:12 PM, soumadwip ghosh <soumadwipghosh at gmail.com>

> Hi all,
>         I have a couple of quick questions. I am simulating DNA duplex with
> some fullerene derivatives. The fullerenes are expected to accommodate
> themselves in the major groove of the DNA and I am getting similar results.
> However, the parallel DNA chains are getting deformed which is also
> expected. My question is apart from H-bonds is there any way by which one
> can show that the DNA is getting significantly deformed as compared to its
> native structure? In the given link below, people have used roll, twist,
> curl and slides to probe the DNA deformation. Is there any way I can
> calculate those parameters from GROMACS?
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439907/pdf/gks517.pdf
> How can I show the time evolution of fraction of native contacts for my DNA
> chain?
> Sorry if I am asking for much. Thanks for your time in advance.
> Regards,
> Soumadwip Ghosh
> Research Fellow,
> India
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