Thanks a lot for the reply.
It would really helpful if you please also mention how would I get the rmsd of
domain 1 w.r.t domain 2.
Thanks once again.
Regards,
Moitrayee
> 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 Sun Sep 26 2010 - 05:00:04 PDT
