Hi,
On Wed, Mar 11, 2015 at 2:09 AM, Robin Jain <robinjain.chem.gmail.com> wrote:
> *trajin prod.mdcrd*
> *center :1*
> *autoimage*
> *rms mass out rms.dat :1*
> *grid test.xplor 20 2 20 2 20 2 :2-65*
> *go*
You have to make sure that you are centering your grid around the area
you're interested. By default the grid is centered at the origin, but
the 'autoimage' command centers to the box center (also, centering
before autoimage/rms is not necessary since things get moved around
anyway). Probably your best bet is to autoimage your molecule of
interest to the origin, e.g.:
trajin prod.mdcrd
autoimage anchor :1 origin
rms mass out rms.dat :1
grid test.xplor 20 2 20 2 20 2 :2-65
Hope this helps,
-Dan
>
> after running i got the file test.xplor and i viewed it with vmd but i got
> a bad plot, which is not showing solvent and solute individual.
> So please help me that what should i do for this.
>
> Thanking You.
> --
> Robin Jain
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--
-------------------------
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 Wed Mar 11 2015 - 08:00:06 PDT
