Here is some explanation of the ion issue
for G-quartets.
Title: Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields
Author(s): Fadrna E, Spackova N, Sarzynska J, et al.
Source: JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 5 Issue: 9 Pages: 2514-2530 Published: SEP 2009
> You should include ions,
> one per each cavity.
> Use Na+ instead, K+ are oversized.
>
> Jiri
>
> -------------------------------------------------------
> Jiri Sponer
> Professor of Biochemistry
> Head of Department of Structure and Dynamics of Nucleic Acids
> Institute of Biophysics
> Academy of Sciences of the Czech Republic
> Kralovopolska 135
> CZ-61265 Brno
> Czech Republic
> e-mail: sponer.ncbr.chemi.muni.cz
> fax: 420 5412 12179
> phone: 420 5415 17133
> http://www.ibp.cz/labs/LSDNA/
> -----------------------------------------------------------
>
>
> > Hi,
> >
> > I have used NMR structure (2kbp) with no K+ ions inside the central tetads.
> >
> > Asfa
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Received on Thu Jun 10 2010 - 07:30:03 PDT
