Hi,
If you would like the RMSD of each individual residue after fitting on
a larger selection this can be done by Cpptraj. Here is an example
input:
parm prmtop
reference inpcrd
trajin mdcrd
rmsd :10-260 reference perres range 10-260 perresout PerResRMSD.dat
This will first perform an overall rms fit of each frame using
residues 10 to 260, then the rmsd of each individual residue in the
range of 10 to 260 will be output to PerResRMSD.dat. Each column in
that file will be the RMSD of a residue. By default the entire residue
is selected; to modify the selection you can specify "perresmask
<mask>". For example, to select only backbone atoms of each residue in
the above example:
rmsd :10-260 reference perres range 10-260 perresout PerResRMSD.dat
perresmask &.C,CA,N
See the manual for more details and keywords, and let me know if you
have trouble getting it to work.
-Dan
On Tue, Jun 7, 2011 at 5:03 AM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
> 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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Received on Tue Jun 07 2011 - 04:30:04 PDT
