Try using cpptraj from AmberTools 13. In this case, you can use the
"autoimage" command in place of the 'center' and 'image' commands you used
below. It looks like your issue may be related to imaging (have you
checked that the imaging looks 'correct' when you view the waters?
In particular, I'm concerned about the use of familiar in one of the
imaging steps and its omission in the other. Familiar imaging is done for
non-orthorhombic cells. The nice thing about "autoimage" is that it
figures out the 'correct' type of imaging that should be done and typically
just "does the right thing".
HTH,
Jason
On Sun, May 19, 2013 at 5:08 AM, BERGY <nucleic81.gmail.com> wrote:
> Dear Sir,
> i am trying to use grid command for calculating water and ion density in
> RNA.
> I followed your instruction given in amber forum. The ouput is given
> below. i have some unusual density seen along the side wall of the
> box. pls suggests.?
>
> http://archive.ambermd.org/201005/0791.html
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> trajin traj.1
> trajin traj.2
> trajin traj.3
> trajin traj.4
> trajin traj.5
> trajin traj.6
> trajin traj.7
> trajin traj.8 1 3000 1
>
> center :1-12 mass origin
> image origin center
> center :1-24 mass origin
> image origin center familiar
>
> rms first mass out rms-grid :4-9,16-21
> grid wat.grid 100 0.5 100 0.5 100 0.5 :WAT.O
> grid na.grid 100 0.5 100 0.5 100 0.5 .Na+
> grid cl.grid 100 0.5 100 0.5 100 0.5 .Cl-
>
> translate x -0.25 y -0.25 z -0.25
>
> average avg.pdb pdb :1-24
>
>
> --tec3
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>
> _______________________________________________
>
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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 21 2013 - 05:00:04 PDT
