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

From: Marek Maly <marek.maly.ujep.cz>
Date: Fri, 27 Jul 2018 15:18:27 +0200


please could someone suggest correct form for mask:


i.e. all atoms belonging to residues with names CEN,RE1,RE2,RE3,END
excluding residues
with numbers from 1036 to 1080 and from 1396 to 1440 ?

I tried the above form and several others with and without brackets




in combination with "radial" command (see below) and in each case it
failed with error below " Not all arguments handled:".

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 ...

Thanks in advance for help,

    Best wishes,


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

Error: [radial] Not all arguments handled: [ STRIP.ptraj ]
         1 errors encountered reading input.
Warning: Set '(:CEN,RE1,RE2,RE3,END)&!(:1036-1080)&!(:1396-1440) =>
(:CEN,RE1,RE2,RE3,END)&!(:1036-1080)&!(:1396-1440)' contains no data.

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Received on Fri Jul 27 2018 - 06:30:03 PDT
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