Hi Xiao Chen,
I think you missed the symbol "!" in your side-chain rmsd calculation.
It should be like this --- rms reference out rmsd_sc.dat: !.N,CA,C,O,H
instead of --- rms reference out rmsd_sc.dat : @N,CA,C,O,H
hope this will solve your problem.
Warm regards
Fredrick.
On Tuesday, June 7, 2011 13:04 CEST, Xiao Chen <chen.xiao.po.gmail.com> wrote:
> Thanks Thomas,
>
> I tried for a particular residue (number 24) as you had suggested,
>
> rms reference out rmsd_bb.dat : 24 .N,CA,C
> rms reference out rmsd_sc.dat : 24 @N,CA,C,O,H
>
>
> The two sets of values are identical :(
>
> Can you please help?
>
> On Tue, Jun 7, 2011 at 4:02 PM, Thomas Gaillard <
> thomas.gaillard.polytechnique.edu> wrote:
>
> > Le Tuesday 07 June 2011 à 02:33:57PM, Xiao Chen a écrit :
> > > Hi All,
> > >
> > > How can we calculate
> > > a)rmsd of each residue (backbone) at each frame in the simulation
> > (not
> > > r.m.s.f).
> > > b)rmsd of only the side-chain at each frame in the simulation .
> > >
> > > Thanks,
> > >
> > > Po
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > You can do it with ptraj using a script similar to this (adapt the
> > selections to your needs):
> >
> > ptraj file.prmtop << EOF
> > reference ref.pdb
> > trajin traj.crd
> > rms reference out rmsd_bb.dat .N,CA,C
> > rms reference out rmsd_sc.dat !.N,CA,C,O,H
> > go
> > EOF
> >
> > --
> > Thomas Gaillard
> > Maître de conférences
> > Laboratoire de Biochimie
> > Ecole Polytechnique
> > 91128 Palaiseau cedex
> > tel: +33 1 69 33 48 62
> > fax: +33 1 69 33 49 09
> > thomas.gaillard.polytechnique.edu
> > http://bioc.polytechnique.fr/~gaillard
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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Received on Tue Jun 07 2011 - 05:00:04 PDT
