TXYZ Arc file parse fails, doesn't recognize periodic boundary box definition

[Dariusrussellkish]

Expected behaviour

Parse Tinker Archive file into a Universe

Actual behaviour

Error on parsing, fails to parse periodic boundary box produced by Tinker on line 2 of each frame.

103
10.000000 10.000000 10.000000 90.000000 90.000000 90.000000
1 OH -4.258215 -1.973780 0.949736 1232 2 10
2 CT -4.263714 -1.766981 2.353863 1063 1 3 11 12
3 CT -2.868573 -1.546285 2.893741 1066 2 4 6 13
4 OS -2.130847 -2.679206 2.594471 1068 3 5
5 CT -0.793726 -2.351497 2.219711 1069 4 7 14 18

Code to reproduce the behaviour

hexanes_arc.zip

import MDAnalysis as mda

u = mda.Universe(top)

....

Currently version of MDAnalysis:

0.18.0

[richardjgowers]

Hi @Dariusrussellkish thanks for reporting this

https://dasher.wustl.edu/tinker/distribution/source/prtxyz.f

It looks like tinker only writes the box in a periodic simulation, so there'll have to be some if statements to see what sort of archive/txyz file this is

[orbeckst]

I label this as a bug because not detecting PBC in an MD format is not good.