there is a very nice tutorial on DNA simulations that
includes RMSD calculations. have you tried that?
the tutorials can be found on the amber web site.
On Jan 19, 2008 8:16 AM, Biman Jana <bjana.sscu.iisc.ernet.in> wrote:
> Dear Users,
> I am doing a temperature dependent study of aqueous dupleax DNA.
> I have a 38 base pairs (76 residue) DNA. I want to calculate the RMSD of
> the DNA at each temperature. I am a new user and know very less about
> calculating RMSD using ptraj or carnal. Can anybody please tell me what
> will be the standard ptraj.in file for this. Any suggestions will be
> highly appreciated.
>
> Biman Jana
>
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Received on Sun Jan 20 2008 - 06:07:33 PST
