Aha! I am definitely not using a symmetric shape matrix (which is weird,
because I got the coordinates from charmm-gui).
I should have posted the XSC contents earlier:
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
0 83.5014512836 0 0 -27.8338170946 78.7259232555 0 27.8338170946
39.3629616277 68.1786494757 0 0 0
The length parameter is definitely that first entry, but the others are
scaled values. I had found a page describing this earlier via google, but
have since lost it.
Is there a fix for this? Can I somehow give parmbox a symmetric matrix for
the same shape?
On Tue, Nov 29, 2016 at 1:26 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Hmm...I'm not sure how NAMD stores unit cell info in the DCD
> trajectory. According to CHARMM, since version 22 the symmetric shape
> matrix is stored instead of unit cell parameters. The weird angle
> you're getting for truncated octahedron makes me suspect that the unit
> cell information in your trajectory is actually unit cell parameters.
> This can be easily tested if you have a version of cpptraj laying
> around < 16.16 - prior to this cpptraj didn't understand the shape
> matrix info output by CHARMM. If this is indeed the case I'll have to
> update cpptraj so it can figure out (or be told) what kind of unit
> cell parameters are in a DCD file.
>
> -Dan
>
> On Tue, Nov 29, 2016 at 1:56 PM, Brian Radak
> <brian.radak.accts.gmail.com> wrote:
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> 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
> > _______________________________________________
> > 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 - 12:00:03 PST
