Mary,
try cpptraj and autoimage first. (actually should always use cpptraj now).
parm your.parm7
trajin your.nc
autoimage
If you want to know if re-imaging is necessary or not, you can convert a
snapshot to pdb and visualize it, check if your molecule looks weird or not.
Please try to read other threads related to autoimage.
Hai
On Fri, Jun 3, 2016 at 6:58 AM, Mary Varughese <maryvj1985.gmail.com> wrote:
> Sir,
>
> I have used iwrap=1 for a simulation. Is the re-imaging commands below ok?
> I want to use ptraj; (autoimage is for cpptraj. isnt?). a dsDNA and ligand.
>
> center :1-20 mass origin
> image origin center familiar
> center :1-40 mass origin
> image origin center familiar
> center :1-41 mass origin
> image origin center familiar
>
> Is this correct.
>
> If i didnt use iwrap=1; then re-imaging is not necessary. Isnt?
>
>
>
> Thanking you
>
> mary
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Received on Fri Jun 03 2016 - 08:00:02 PDT
