Hi Daniel
Thanks. I used this command:
nativecontacts :1-356 mindist out mindist.dat
But I have following doubts:
1) Manual says 'nativecontacts' needs a reference structure so that it
would mean I need to update reference structure (reference would be the
same as the frame to be analysed) but in case of distance calculation why
one would need that?
2) Also am always getting 0.96 as mindist which I think is the distance of
hydrogen bonded to some atom (of structure in the unit cell). but I am
interested in knowing distances of atom pairs with image rather in the unit
cell itself.
On Mon, Jun 2, 2014 at 3:50 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You can use the new 'nativecontacts' command in cpptraj with the
> 'mindist' keyword to calculate the minimum distance seen either within
> a single group of atoms or between two groups of atoms. Imaging is on
> by default for this command when box coordinates are present unless
> the 'noimage' keyword is specified.
>
> Hope this helps,
>
> -Dan
>
> PS - You can also find the maximum distance with the 'maxdist' keyword.
>
> On Mon, Jun 2, 2014 at 8:46 AM, newamber list <newamberlist.gmail.com>
> wrote:
> > Hi All
> >
> > This is an old mail regarding minimum distance between the images:
> >
> > http://archive.ambermd.org/200501/0024.html
> >
> > I am just wondering is it implemented now? I need to know the minimum
> > distance between the images and I can script down to calculate for each
> > pair of atoms but would be good to know if any inbuilt command can help
> in
> > that?
> >
> > thanks in advance
> > JIom
> > _______________________________________________
> > 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 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Mon Jun 02 2014 - 09:00:02 PDT
