[gmx-users] pdb2gmx and periodic molecule

[Alex]

Ahoy,

What I have here is a 100% precisely set up periodic ssdna chain of
six residues without termini. The goal is to get the 'polymerization'
across the box. So, I boxed the chain and set up the periodicity pretty much
perfectly.

To test, translation in the direction of periodicity by the
periodicity constant results in bonds perfectly recognized by things like VMD or
pymol (in the concatenated structure).

When running pdb2gmx on the boxed structure, the periodicity seems to
be ignored and then expectedly I get a fatal error with a custom FF that works
fine on finite chains.
x2top sees pbc, but we're not using it here. So, no topology in sight.

Any ideas?

Thanks,

Alex

p.s. I can post the test structure if there's any doubt about periodicity
of the structure itself.