Re: [AMBER] The right syntax for creating the given mask using logical operators - Not all arguments handled

From: Daniel Roe <>
Date: Fri, 27 Jul 2018 11:51:28 -0400


On Fri, Jul 27, 2018 at 9:18 AM, Marek Maly <> wrote:
> Hello,
> please could someone suggest correct form for mask:

I don't think the problem is with the atom mask:

> Error: [radial] Not all arguments handled: [ STRIP.ptraj ]
> 1 errors encountered reading input.

This error message indicates the actual issue is that you have extra
unhandled stuff ('STRIP.ptraj') on the 'radial' command line.

> radial RDF_DEN_DENmimoOdtrzeneDen.txt 0.25 150 (:CEN,RE1,RE2,RE3,END)&!(:1036-1080)&!(:1396-1440) (:CEN,RE1,RE2,RE3,END)&!(:1036-1080)&!(:1396-1440) noimage nointramol >> STRIP.ptraj

I'm not sure why you have a UNIX redirect on the 'radial' command line
but that certainly won't work. The way you have written the command
doesn't correspond to any accepted syntax for 'radial'. It appears you
are using the old PTRAJ style, which is:

radial <output_filename> <spacing> <maximum> <mask1> ...

Note that the order matters here. I recommend upgrading to the latest
version of cpptraj if you haven't already and use the new syntax,
which is much more forgiving:

> help radial
  [help radial]
    [out <outfilename>] <spacing> <maximum> <solvent mask1> [<solute
mask2>] [noimage]
    [density <density> | volume] [center1 | center2 | nointramol] [<name>]
    [intrdf <file>] [rawrdf <file>]

In either case, get rid of the '>> STRIP.ptraj' part of the command.

Also note that in your mask you can combine the residue number lists, e.g.


> It seems that for this logic construction there is not good example in
> manual and
> as I also already wasted some time by searching some useful info in Amber
> mailing list I have to say that this syntax is not too much intuitive and
> clear ...

In the future, you can make use of the 'select' command (or even
'atoms' etc commands) to test mask syntax beforehand. But again, mask
syntax doesn't seem to be your issue here.


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Received on Fri Jul 27 2018 - 09:00:04 PDT
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