AMBER Archive (2008)

Subject: Re: AMBER: ptraj selection

From: David Watson (dewatson_at_olemiss.edu)
Date: Wed Jul 09 2008 - 22:59:27 CDT

On Jul 9, 2008, at 10:13 PM, Ilyas Yildirim wrote:

> 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.
>

I can only refer you to the 'ambmask' section of the Amber Users'
Manual, as that is all that I can find on the matter.
Braces are definitely verboten, whereas parentheses are permitted, but
I don't see where quotes are permitted.

Perhaps use the parentheses without quotes?

> --
> Ilyas Yildirim
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