AMBER Archive (2008)

Subject: Re: AMBER: ptraj selection

From: David Watson (dewatson_at_olemiss.edu)
Date: Wed Jul 09 2008 - 21:11:16 CDT

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.

> PS: This is an RNA single strand of GACC.
>
> --
> Ilyas Yildirim

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