Hi,
First of all, you can not plot them with amber. If you want to make
this sort of an analysis you can write down a script. Just as a quick
and dirty way of doing it, you can proceed with this;
If base pairs are disappearing, also phosphates disappearing. Then
read the documentation on amber trajectory analysis package "PTRAJ",
which in fact comes with ambetools i believe. Relaying on this info,
write script and find the trajectories of phospahates in your system.
Try to find a way of measuring the distances among those. This can be
easily done by another script by the way. With all those in hand, you
can decide at which point your strand starts melting. You can also
have enough info about the number of remaining basis. When you get all
those if you are running a linux based operating system, you can plot
those numbers with respect to the time by using any simple plotting
program (i.e. gnuplot, xmgrace etc...).
I believe this was the 100th time that i saw this question. I hope
those can help...
best
peker
On Mon, Jan 17, 2011 at 8:49 AM, david condon <dec986.gmail.com> wrote:
> Hi Shesh,
>
> I'm not sure if you just want to find a computational way of finding
> these, but these can easily be calculated without AMBER.
>
> You can find a tool at
> http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/ where you
> can input your concentration and sequence, and it will give you the
> melting temperature.
>
> There are papers on the subject, which you can find with google
> scholar, scifinder, etc.
>
> Hope this helps,
> -Dave
>
> On 1/16/11, Shesh Nath <sheshnath65.gmail.com> wrote:
>> Dear Sir
>> I have heated 10-mer DNA .I want to determine the melting point of
>> DNA. For this I want to plot a graph between No.of base pairs and
>> Temperature.
>> How can I plot this graph using Amber10.
>> please help me.
>>
>>
>> --
>> SHESH NATH
>> RESEARCH SCHOLAR,
>> THEORETICAL CONDENSED MATTER PHYSICS,
>> DEPARTMENT OF PHYSICS,
>> BANARAS HINDU UNIVERSITY,
>> VARANASI-221005
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Mon Jan 17 2011 - 07:30:04 PST
