[gmx-users] pdb2gmx "dangling bond" error when trying to make periodically connected DNA

[Viveca Lindahl]

Hi,

I'm trying to create a topology for DNA with periodically connected ends.
There's a previous message on this, with advice by Justin:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096970.html

I have a single-stranded DNA structure in a pdb file with a phosphate on
one end (P, OP1, OP2) and an oxygen on the other (O3'). These are exactly
the atoms I want to connect later on. I use pdb2gmx to get the hydrogens +
topology and give it -ter "none", which gives me the error message

"Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry."

I added the flag -missing (according to Justin's advice), but does not
help. I guess I'm not understanding what bond is dangling here, and what to
add to the tdb file that would help?

Of course, I could get most of the topology I need by avoiding selecting
-ter 'none' but then I have to fiddle with adding back atoms.

Best,
Viveca