AMBER Archive (2009)

Subject: [AMBER] DNA simulation: Problem with RMSD

From: BERGY (nucleic81_at_gmail.com)
Date: Wed Mar 04 2009 - 21:44:26 CST

Dear Amber users,

 I am doing a MD simulation on a 12mer DNA, for all my RMSD ,
helicoidal analysis i wish to remove the terminal base pairs from the
analysis. How to go about.
--------------------------------------
(this a sample input)
trajin traj1.mdcrd
trajin traj2.mdcrd
trajout fixed.traj
rms first out rms :2-11,13-23 time 0.2
center :1-24
image
strip :WAT
go
---------------------------------------
Is the format correct to calculate RMSD. will my fixed.traj output
file have the terminal base pairs removed.

regards
dksenthil,

Graduate Student
MBU,IISc,
Bangalore,
India

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