Dear Amber !
I have tried the junction structure using both igb =1 and igb=2 ,
In both the cases the junction was very stable for 2 to 3 nanoseconds and
then it started to open up from the
closed state and it stayed for some 4 ns and after that it came out as 2 + 2
duplexes and the duplexes had only 3-4 base pairs
paring to each other and the other are far apart it has 10 Base pairs .
I have a doubt , how should one procede for the formation of the duplexex
is it posible by gb ,
i tried its not working !
what one can do !
regards
maya
On Thu, Apr 8, 2010 at 8:29 PM, case <case.biomaps.rutgers.edu> wrote:
> On Thu, Apr 08, 2010, maya maya wrote:
> >
> > I would like to know does any one have tried
> > the GB simulation for the Holliday Junction .
>
> > Is it possible to do with amber !
>
> We have lots of unpublished studies of Holliday junctions using igb=1.
> It's certainly possible!
>
> ...dac
>
>
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Received on Fri Apr 09 2010 - 00:00:02 PDT
