Thanks Dan!
The syntax of the rmsd command as you suggested does not work :(
Did you mean :
rms :10-260 reference perres range 10-260 perresout PerResRMSD.dat
The Amber11 manual has no mention of the perres keyword so im having a tough
time figuring this out. Could you please help out because your description
of the output (Each column in that file will be the RMSD of a residue) is
exactly what i need.
Yours,
Po
On Tue, Jun 7, 2011 at 4:37 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Tue Jun 07 2011 - 22:00:03 PDT
