Dear Daniel and Jason
Thanks it works :1<.3.6&.Cl- ( <. is all atoms, within 3.6 distance and &.Cl- is all Cl- ); I messed it before
>> Note that the distance-based mask uses the active reference structure in parsing the mask, i.e. it does not update on a frame-by-frame basis.
So that would mean for a trajectory I have to provide 'reference' each time and then average over all bins by own script.
thanks
Jiomm
On Thursday, April 3, 2014 11:49 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
On Thu, Apr 3, 2014 at 4:27 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Apr 3, 2014 at 5:57 PM, Jio M <jiomm.yahoo.com> wrote:
>
> > Hi All
> >
> > I am using this cpptraj command:
> >
> > radial rdf_wat 0.1 10 :WAT (:1 <:Cl- 3.6) volume
> >
>
> Put quotes around the mask. If there are spaces, the parser will split on
> whitespace.
>
Also, ':1<:Cl-3.6' is not a valid distance-based mask. You probably want
something like ':1<:3.6&.Cl-'; see section 8.2.3 "Atom mask Selection
Syntax" of the AmberTools 13 manual for more details. Note that the
distance-based mask uses the active reference structure in parsing the
mask, i.e. it does not update on a frame-by-frame
basis.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Apr 03 2014 - 18:00:02 PDT
