You must have ions there, there is no G-stem without
ions, this is the dominant stabilization.
Title: Molecular dynamics simulations and their application to
four-stranded DNA
Author(s): Sponer, J; Spackova, N
Source: METHODS Volume: 43 Issue: 4 Pages: 278-290 Published: 2007
Jiri
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> Hi,
>
> Thanks for all your suggestions. I tried the following with pdb id: 2kbp
>
> tleap -s -f leaprc.ff99bsc0
> loadoff RNA_CI.lib
> dna = loadpdb ....
> ...
>
> I carried out a production run for 6ns after all the haeting and
> equilibration runs and again at the beginning of the run, the two strands
> split open as shown in the attachment.
>
> As suggested, I'll try by incorporating central Na+ ions.
>
> Asfa.
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Received on Fri Jun 11 2010 - 04:30:09 PDT
