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
Received on Tue Nov 29 2016 - 10:30:03 PST
