AMBER Archive (2007)

Subject: AMBER: Targetted MD and ptraj analysis

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Sep 19 2007 - 00:47:19 CDT

Dear AMBER users,

I have the following ptraj script, which is first alligning the structure
on the specified atoms, and then calculating the RMSD for the specified
atoms.
---- ptraj.in ------------------------------
trajin mdcrd_01.traj.p1.gz
rms first out rms_out :1-16_at_P,O?',C?'
strip :WAT,Na+
principal :1-16 mass
go
--------------------------------------------
Unfortunately, this does not work. I am trying to analyze a targetted MD
simulation, and wondering if it is possible in ptraj to (1) first
alligning the structure on specified atoms, and then (2) calculating the
rmsd of the chosen atoms. Thanks.

Best, 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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