[AMBER] Problem in MD simulations of DNA using ABC protocol

From: abc def <biotechabc.gmail.com>
Date: Tue, 9 Nov 2010 23:24:25 +0530

Hi all,

I am trying to do MD simulations on a B-DNA using the same protocol as
described in the paper (Ascona B-DNA Consortium)

*Paper :* Molecular Dynamics Simulations of the 136 Unique Tetranucleotide
Sequences of DNA Oligonucleotides. I. Research Design and
Results on d(CpG) Steps. Beveridge et.al. Biophysical Journal (87) - 2004.


But after running the simulations for 5 ns, I found out that my structure is
distorted in the sense that the rings of bases are no longer planar. Can you
tell me where I am making the mistake or is their the problem in the
visualizer (I am using Pymol and ViewerPro for visualizing the structures) ?

I am attaching the pdb file genrated after 5ns simulation along with this
mail.

Kindly let me know where I am going wrong, because I have tried this
protocol on 2-3 system and the same thing is happening.

Thanks in anticipation,

Regards,


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Received on Tue Nov 09 2010 - 10:00:04 PST
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