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
> > _______________________________________________
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>
> 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
>
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>
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Received on Tue Jun 07 2011 - 04:30:03 PDT
