AMBER Archive (2008)

Subject: Re: AMBER: RMSD calculation using AMBER7

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Jan 19 2008 - 08:19:45 CST

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_at_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
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

amber.scri

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu