AMBER Archive (2008)

Subject: Re: AMBER: ptraj selection

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Jul 09 2008 - 22:13:22 CDT

On Wed, 9 Jul 2008, David Watson wrote:

> On Jul 9, 2008, at 8:07 PM, Ilyas Yildirim wrote:
>
> > 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.
> >
>
> I think the problem lies with the use of quotes and parentheses.

Can you explain a little bit more? If I do not use the quotes and
paranthesis, ptraj won't read the part after the first '|'. Thanks. 

-- 
  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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