[AMBER] Domainwise rmsd using ptraj rms

From: <moitrayee.mbu.iisc.ernet.in>
Date: Thu, 16 Sep 2010 01:55:54 +0530 (IST)

Dear Amber Users,

I want to calculate domainwise RMSDs using ptraj, i.e RMSD of domain a w.r.t
domain a, and so on.

I am using the following script.

......
......
trajin xxxx.9990_10000.crd

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

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 - 13:30:03 PDT
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