I just downloaded AmberTools16 today, Cpptraj V16.16.
There are probably a number of places weird things could happen. Maybe the
following observations are relevant:
1) the CHARMM PSF format does not include *any* box information
2) the extended system (xsc) file that I used in my simulation weirdly has
all zeros for the angles (I guess because NAMD uses (can use?) a full
vector specification instead?)
3) I have little idea as to how the DCD trajectories store box information
4) this was a constant volume simulation
On Tue, Nov 29, 2016 at 12:48 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak.anl.gov
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Received on Tue Nov 29 2016 - 11:00:03 PST
