Hi,
On Wed, Sep 15, 2010 at 4:25 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> rms first :1-120.CA out rms_domain1
> rms first :121-218.CA out rms_domain2
> rms first :219-343.CA out rms_domain3
> rms first :344-483.CA out rms_domain4
In each case you are calculating the RMSD of the specified region in
each frame to that same region in the first frame. If you wanted rmsd
of domains 1-4 w.r.t. the whole first structure you'd do something
like:
rms first :1-483.CA out rms_all
rms first :1-120.CA out rms_domain1 nofit
etc
In this case you're fitting the coords on the entire protein. The
'nofit' option prevents ptraj from rotating and translating the
coordinates. Hope this helps clear things up.
-Dan
>
> center .CA
> strip :WAT
>
> go
>
> where 1-120 is domain 1, and so on.
>
> My reference structure is first, but with this script am I getting interdomain
> RMSDs or is this script generating RMSDs of domain 1...4 w.r.t the whole first
> structure?
> I am a little confused.
> Any suggestions will be of immense help.
>
> Thanks a lot in advance.
>
> Best Regards,
> Moitrayee
>
>
>
>
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Received on Wed Sep 15 2010 - 15:00:03 PDT
