Thank you Dr. Ross ,
but how to mention for all atoms ,
they have given in archives like
rms first out complex_equi3.crd.rmsd .CA,C,N
what have to be given after . ,
thankyou
regards
balaji
UOM
> From: ross.rosswalker.co.uk
> To: amber.ambermd.org
> Subject: RE: [AMBER] rmsd_ptraj
> Date: Wed, 8 Jul 2009 21:35:59 -0700
>
> 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 - 01:09:34 PDT
