Hi balaji,
See the 'reference' command in the manual
trajin foo.mdcrd
reference foo.rst
rmsd reference ...
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of balaji nagarajan
> Sent: Wednesday, July 08, 2009 9:20 PM
> To: amber forumnew
> Subject: [AMBER] rmsd_ptraj
>
>
> Dear Amber ,
>
> I have looked in to the archive , for calculating rmsd of the
> trajectory with respect to the first frame
>
> but ,
>
> I would like to calculate the rmsd of the trajectory which i have
> generated in the
> simulation , with respect to the model which i built ,
>
> I have minimised and equillibriated my model and now i have the
>
> model.rst file and the trajectory file traj.mdcrd
> is it possible to calculate the rmsd of each frame of the trajectory ,
> with this
> model file (model.rst ) .
>
> I f so how one should give the ptraj input file
>
> thank you
> regards
> balaji
>
>
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Received on Thu Jul 09 2009 - 01:09:04 PDT
