Hi,
You need to use the 'mask' and 'mask2' keywords to specify your masks.
The onboard help shows the correct syntax:
> help pairdist
out <filename> mask <mask> [mask2 <mask>] [<resolution> delta]
Calculate pair distribution function P(r) between two masks.
Hope this helps,
-Dan
On Mon, Nov 17, 2014 at 7:49 AM, DEBOSTUTI GHOSHDASTIDAR
<debostutighosh.gmail.com> wrote:
> Dear Amber Users
>
> I was trying to use pairdist function to compute the distribution of
> distance between two sets of atoms. So the command I gave was as follows:
>
> pairdist out ring :MOL.N1,N2,C1,C2,C3 :MOL.N1,N2,C1,C2,C3 0.1
>
> However on execution i get an error saying
> Error: pairdist: No mask1 specified.
>
> Is there a particular way of specifying the mask? Couldn't figure out from
> the manual.
>
> Also, when I give a set of atoms, does the function consider the
> center-of-mass?
>
> Thanks for any help
>
> --
> Debostuti Ghosh Dastidar
> Department of Biotechnology
> Indian Institute of Technology Madras
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Mon Nov 17 2014 - 07:30:02 PST
