I can confirm that this works as advertised. Kudos for the fast turnover!
Is there any chance that you would ever write Tcl frontend for cpptraj to
be used in VMD (just autoimage would be fantastic)? Their pbctools package
is pretty nice, but lacks this very desirable functionality -
non-orthorhombic boxes for all!
Brian
On Wed, Nov 30, 2016 at 1:18 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Please try the GitHub version of cpptraj:
> https://github.com/Amber-MD/cpptraj. I just added two new keywords to
> 'trajin' for CHARMM trajectories: 'ucell' to force reading box info as
> unit cell params, and 'shape' to force reading box info as shape
> matrix. So you should be able to do:
>
> trajin mytraj.dcd ucell
>
> to get it to read the box as unit cell params. If you get a chance to
> try it and it works (or doesn't), let me know. Thanks,
>
> -Dan
>
> On Tue, Nov 29, 2016 at 4:02 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > If you can use the older version of cpptraj for now that is the
> > quickest workaround. I will try to get something going over the next
> > day or so. Thanks,
> >
> > -Dan
> >
> > On Tue, Nov 29, 2016 at 2:34 PM, Brian Radak
> > <brian.radak.accts.gmail.com> wrote:
> >> 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
> >> _______________________________________________
> >> 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
>
>
>
> --
> -------------------------
> 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 Fri Dec 02 2016 - 14:00:02 PST
