Hi Daniel
I have written a script than can handle each pdb file (obtained from trajectory) and do required analysis but its limited to single imaged box.
I would like to consider the waters/ions in pbc as well but what I get in pdb is the single central imaged box. This was the reason, in other mail I sent, I wanted to know how to print coordinates for the surrounding boxes (14 surrounding +1 central boxes for a truncated octhedron).
thanks
JIom
P.S. Actually I am making cylindrical grids (this is how my script works and cpptraj as of now makes rectangular grids only) and the cylinder would cross the truncated octahedron box if I increase the diameter. So I need to include the imaged boxes as well.
thanks
Jiom
On Thursday, April 3, 2014 9:10 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
Hi,
I don't think there is currently any way to do this (simply) in Amber. You
could certainly think about either writing a program in NAB or something,
but all distance calculation routines are currently three dimensional.
-Dan
On Thu, Apr 3, 2014 at 1:35 PM, Jio M <jiomm.yahoo.com> wrote:
> Hi All
>
> I am wondering can we measure distances in one plane over whole trajectory
> in AMBER? I want to do some analysis with distances being measured by
> ignoring z dimension (that is first projecting all atoms in xy plane and
> then calculate distances for some analysis).
>
> best regards
> 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 03 2014 - 14:00:02 PDT
