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
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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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Received on Tue Jun 07 2011 - 04:00:02 PDT
