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
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Received on Tue Nov 29 2016 - 13:30:02 PST
