> On May 17, 2014, at 12:41 PM, newamber list <newamberlist.gmail.com> wrote:
>
> Hi All,
>
> I am running rmsd with cpptraj (14.0) but getting these warnings (even I
> use imaged or non-imaged traj). Though as suggested imaging is not required
> for rmsd option
>
> cpptraj input:
>
> trajin traj.nc #OR trajin imaged_traj.nc
> reference initial.inpcrd
> rms reference mass :1-324 out rms.dat
>
>
> Warning: Coordinates are being rotated and box coordinates are present.
> Warning: Unit cell vectors are NOT rotated; imaging will not be possible
> Warning: after the RMS-fit is performed.
>
>
> I dont get these warnings when I simply image my traj as
>
> trajin traj.nc
> center origin :1-324
> image origin center familiar
> trajout imaged_traj.nc
>
>
> Thanks for any help
Help with what? You didn't ask a question. The warning is self-explanatory. When you do a RMS fit, you rotate the system which ruins periodic box vector alignment. So you won't be able to image after you RMS fit. You can certainly image before you do that...
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat May 17 2014 - 11:00:03 PDT
