Thanks...
On Mon, Nov 17, 2014 at 8:47 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Debostuti Ghosh Dastidar
Indian Institute of Technology Madras
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Received on Mon Nov 17 2014 - 22:00:03 PST
