RMSD can be measured in different terms what you mean to in each case you
want RMSD vs. time or is it in each case RMS from starting structure. Both
you can do by CPPTRAJ. Check through amber keywords for RMSD
use perres keyword as previously mentioned. If you want against some
reference use something like this
reference xxx/min.rst
trajin strip.bps
rms reference out rms-min.dat .CA
average av.pdb * pdb nobox
It depends what you want because if you edit the keyword you can get a
desired result.
On Sat, Jun 28, 2014 at 3:16 AM, Chinthaka Ratnaweera <cnr88.msstate.edu>
wrote:
> This is not I meant.
> Lets say, I have two pdb structures of the same protein, which generated
> through average md trajectories after different interactions. These two
> structures are slightly different. I want to find out the rmsd between
> them. I know VMD can do that. But I want to know whether it is possible in
> ptraj or cpptraj?
>
>
> On Fri, Jun 27, 2014 at 4:19 PM, Soumendranath Bhakat <
> bhakatsoumendranath.gmail.com> wrote:
>
> > Check with this
> > trajin md1.mdcrd
> > atomicfluct out RMSF :1-198 byres
> > change the residues as u want
> >
> > On 6/28/14, Chinthaka Ratnaweera <cnr88.msstate.edu> wrote:
> > > I want to calculate per residue rmsd between two proteins. Can it be
> done
> > > using ptraj?
> > >
> > > Thanks
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Thanks & Regards;
> > Soumendranath Bhakat
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Fri Jun 27 2014 - 16:00:03 PDT
