To add to this I think the density of the system needs to be specified.
On Fri, May 7, 2010 at 8:43 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Postdoctoral Associate
> SAS - Chemistry & Chemical Biology
> 610 Taylor Road
> Piscataway, NJ 08854
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>
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Received on Fri May 07 2010 - 06:00:28 PDT
