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
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 15 2010 - 13:30:03 PDT
