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

From: Marek Maly <>
Date: Sat, 28 Jul 2018 14:39:02 +0200

Hi Daniel,

first of all thanks a lot for prompt help !

Dne Fri, 27 Jul 2018 17:51:28 +0200 Daniel Roe <>

> Hi,
> 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.

Yes you are right I overlooked ">> STRIP.ptraj" term in my "ptraj" file.

The reason why this redirection was here was that originally the
file was automatically created by primary script, where was e.g. line:

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

But here when I used that complicated mask containing e.g. brackets linux
wrote an error:

./ line 28: syntax error near unexpected token `('
./ line 28: `echo radial RDF_DEN_DENmimoOdtrzeneDen.txt 0.25 150
(:CEN,RE1,RE2,RE3,END)&!(:1036-1080)&!(:1396-1440) noimage nointramol >>

so just the simple copy command: echo amber_command >> STRIP.ptraj was
not performed in this case due to the some linux-syntax problem. It seems
that linux command "echo" has some problem to copy this command containing
characters like (),:,&,! from some reason and probably whole amber_command
has to be placed into "" or another brackets, or so ...

If you could suggest solution here I would be grateful.

If I use the same construction i.e. echo amber_command >> STRIP.ptraj in
my primary script to copy
other commands , including that radial (without such complicated masks) it
works prefect.

So from this reason I prepared input file STRIP.ptraj by hand, deleted
"echo" command but forget
to delete the " >> STRIP.ptraj" at the end of line.

The problem was that first time I prepared "STRIP.ptraj" by hand right (so
deleted also >> STRIP.ptraj ) and reported error was really focused on
mask (some early wrong version), then I experimented with mask but by
mistake deleted "STRIP.ptraj" file and so created by hand second time,
now with that mistake i.e. forgotten redirection term which I overlooked
and since that I did not control in detail amber errors so did not learn
that the problem is not now with mask but with nonsense keyword.

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>]

Sorry but here I dont see any difference between:

radial <output_filename> <spacing> <maximum> <mask1> <mask2> ...


radial [out <outfilename>] <spacing> <maximum> <solvent mask1> [<solute>

There is in my opinion the same order of arguments in both versions.

I am using cpptraj as implemented in Amber16 or more precisely in Amber
Tools 17 and had
previously no errors/problems regarding used "radial" command syntax.

So could you be more specific here please,

   Thanks a lot again !

      Best wishes,


> 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.
> (:CEN,RE1,RE2,RE3,END)&!(:1036-1080,1396-1440)
>> 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.
> -Dan
> _______________________________________________
> AMBER mailing list

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Received on Sat Jul 28 2018 - 06:00:03 PDT
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