Hi,
What version of cpptraj are you using? Something is clearly off since
those are definitely not angles for a truncated octahedron cell.
-Dan
On Tue, Nov 29, 2016 at 1:24 PM, Brian Radak
<brian.radak.accts.gmail.com> wrote:
> I have a NAMD DCD trajectory and PSF generated with triclinic boundary
> conditions corresponding to a truncated octahedron, but am having trouble
> getting the trajectory into "familiar" form via cpptraj (which is
> apparently the only utility around that can handle this procedure?).
>
> I did the following:
>>> cpptraj -p my.psf -y my.dcd
>
> Which gave the following helpful warning:
>
> Warning: Trajectory box type is 'Non-orthogonal' but topology box type is
> 'None'.
> Warning: Setting topology box information from trajectory.
>
> Then
>>> autoimage
>>> trajout my.rewrap.dcd
>>> go
>
> However, loading the output dcd into VMD instead shows an orthorhombic cell
> with missing slabs at a diagonal. I checked that the a/b/c/alpha/beta/gamma
> were what I thought they should be:
>>> parmbox
> Box: 'Non-orthogonal' XYZ= { 83.503 83.503 83.503 } ABG= {
> 89.54 89.54 90.46 }
>
> Which did not seem right, so I tried again with:
>>> parmbox truncoct 83.503
>
> but this has the same result. I saw indications in the list archive that
> similar things have been encountered before, but no obvious solutions. Any
> ideas?
>
> Thanks,
> Brian
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Nov 29 2016 - 11:00:02 PST
