Dear All,
I have the following ptraj script:
----------------------------
trajin gacc_nowater_all.mdcrd.gz
rms first out rmsd.all.heavy "(:1-4.C1',C2',C3',C4',C5',O4',O5',O3',P) | (:1,2.N9,C8,C4) | (:3,4.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.C1',C2',C3',C4',C5',O4',O5',O3',P) | (:1,2.N9,C8,C4) |
(:3,4.N1,C2,C6)"
Mask [(:1-4.C1',C2',C3',C4',C5',O4',O5',O3',P) | (:1,2.N9,C8,C4) |
(:3,4.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.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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Received on Sun Jul 13 2008 - 06:07:18 PDT
