AMBER Archive (2007)

Subject: Re: AMBER: DNA structure analysis

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed Jan 17 2007 - 10:23:08 CST

Dear Sponer,

Thank you very much for your advices. As I am new to MD, could you mind to
suggest the right lenght of time for the MD calculations like this?

Best regards,

FM

>From: Jiri Sponer <sponer_at_ncbr.chemi.muni.cz>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: DNA structure analysis
>Date: Wed, 17 Jan 2007 11:39:36 +0100 (MET)
>
>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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