Masks need to be one continuous string, so remove the spaces between the
ampersands, e.g.:
radial radial_file 0.1 7.0 :ISO&(!.H=) :1-161&(!.H=)
The parentheses probably aren't necessary, but then again they don't hurt
and they help readability. As always check the "Mask X represents N atoms"
to make sure Ptraj is actually selecting what you want. Let me know if that
doesn't work for you.
-Dan
On Thu, May 6, 2010 at 9:41 PM, Jose Borreguero <borreguero.gmail.com>wrote:
> Dear Amber/Ptraj users
>
> I am trying to compute the radial distribution function between the heavy
> atoms of two atom sets. Here's the ptraj input file
>
> trajin crdfile
> radial radial_file 0.1 7.0 :ISO & !.H= :1-161 & !.H=
>
> The solvent mask is [:ISO & !.H=], the solute-mask is [:1-161 & !.H=]
>
> Every time I try to run ptraj I have the following error:
> ...
> PTRAJ: radial radial_DHFR_ISO 0.1 7.0 :ISO & !.H= :1-161 & !.H=
> Mask [:ISO] represents 4836 atoms
> Error: illegal binary operation
>
> I've tried other binary operations but always obtain the same error. Is the
> 'radial' function capable of parsing masked expressions involving the '&'
> symbol?
>
> Best regards,
> -Jose
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>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Fri May 07 2010 - 06:00:22 PDT
