From: Giacomo Fiorin (
Date: Wed Nov 24 2021 - 16:47:45 CST

Hi Brian, I'm not sure if there is a pre-cooked tool, but MDAnalysis does
read TPR files:;!!DZ3fjg!sF8fHozb7Go25G7u8XSD0Z7Q6rWB1ttRInyGFW7ayJjfWnK1UBMVSbJd_OWVsH2bJQ$
including bond information.

>From there, with a bit of Python code you can write out a Tcl script that
re-creates all correct bonds in VMD. Use e.g. TopoTools for this purpose:

After loading in VMD the coordinate file with autobonds off:
you can source that Tcl script to create the bonds.

I wouldn't try to do anything more than connecting atoms, and specifically
avoid converting other metadata such as atom types, bond types, etc.
Converting full topologies is one of those tasks where even if you get it
99.9% right it is still not usable.


On Wed, Nov 24, 2021 at 3:56 PM Bennion, Brian <> wrote:

> Hello All
> Just curious if anyone has coded up a plugin to read gromacs connectivity
> information from either top or tpr files?
> Using the gro file as the source of truth creates bonds according to the
> bond table in VMD which may work most of the time. However, there are cases
> for instances where a gromacs simulation explodes and the resulting debug
> pdb step files that are written can appear pretty strange in vmd and
> complicate forensics.
> Reading through the list i found a number of entries with gromacs
> mentioned, although none contained a conversation about gromacs reading
> topology files.
> If I missed something please let me know by replying with the RTM and a
> possible page link.
> thank you
> happy thanksgiving
> brian