AMBER Archive (2008)

Subject: AMBER: ptraj selection

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Jul 09 2008 - 20:07:39 CDT

Dear All,

I have the following ptraj script:

----------------------------
trajin gacc_nowater_all.mdcrd.gz
rms first out rmsd.all.heavy "(:1-4_at_C1',C2',C3',C4',C5',O4',O5',O3',P) | (:1,2_at_N9,C8,C4) | (:3,4_at_N1,C2,C6)"
-----------------------------
(The second part of the script is one line).

The ptraj output selects the wrong atoms. Here is the ptraj output:

----------------------------------------------
PTRAJ: rms first out rmsd.all.heavy
"(:1-4_at_C1',C2',C3',C4',C5',O4',O5',O3',P) | (:1,2_at_N9,C8,C4) |
(:3,4_at_N1,C2,C6)"
Mask [(:1-4_at_C1',C2',C3',C4',C5',O4',O5',O3',P) | (:1,2_at_N9,C8,C4) |
(:3,4_at_N1,C2,C6)] represents 23 atoms
[No output trajectory specified (trajout)]

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 100000 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (gacc_nowater_all.mdcrd.gz) is an AMBER trajectory (with box info)
with 100000 sets

NO OUTPUT COORDINATE FILE WAS SPECIFIED

ACTIONS
  1> RMS to first frame using no mass weighting
      Dumping RMSd vs. time (with time interval 1.00) to a file named
rmsd.all.heavy
      Atom selection follows :1-4_at_P,N1,C2,C4,C5,C6
----------------------------------------------

Can someone tell me what the mistake in the ptraj script is? Thanks a lot.

PS: This is an RNA single strand of GACC. 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Physics        -                              =
  = University of Rochester      -                              =
  = 585-275-6766 (office)        - 585-267-5644 (home)          =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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