[AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD

From: Brian Radak <brian.radak.accts.gmail.com>
Date: Tue, 29 Nov 2016 12:24:05 -0600

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
Warning: Setting topology box information from trajectory.

>> 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


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
AMBER mailing list
Received on Tue Nov 29 2016 - 10:30:03 PST
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