AMBER Archive (2007)

Subject: Re: AMBER: DNA structure analysis

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Wed Jan 17 2007 - 04:39:36 CST

I would first strongly suggest to make a longer simulation!

I think curves as well as 3DNA are appropriata softwares
for DNA.

Best regards

-------------------------------------------------------
Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer_at_ncbr.chemi.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/labs/LSDNA/
-----------------------------------------------------------

> Dear Sir/Madam,
>
> I have done a 1 ns MD for a DNA-intercalator structure, I could like to
> analysis the twist, rise, roll of the flanking base pair and the sugar
> puckering along the trajectory. Could you mind to teach me how to do this
> with amber or any other free softwares?
>
> Thank you!
>
> Best regards,
>
> FM
>
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