VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Fri Nov 26 2021 - 18:38:58 CST

If it also really absolutely HAS to work natively into VMD, I’ve got a tpr plugin that reads about 95% of GROMACS TPR files, which at least one other person has found useful.

https://urldefense.com/v3/__https://github.com/jvermaas/vmd-tprreader__;!!DZ3fjg!rOr5uRQ-B2SQp6Jhf9JUywdQTOCdee740CSdyelOz2mTPjlevyRBYuNGnOlPAVYedw$

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Date: Wednesday, November 24, 2021 at 6:46 PM
To: "Bennion, Brian" <bennion1_at_llnl.gov>
Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: support for gromacs topology files

Hi Brian, I'm not sure if there is a pre-cooked tool, but MDAnalysis does read TPR files:
https://urldefense.com/v3/__https://userguide.mdanalysis.org/1.1.1/formats/reference/tpr.html__;!!DZ3fjg!rOr5uRQ-B2SQp6Jhf9JUywdQTOCdee740CSdyelOz2mTPjlevyRBYuNGnOkdkbNQzg$ <https://urldefense.com/v3/__https:/userguide.mdanalysis.org/1.1.1/formats/reference/tpr.html__;!!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:
https://www.ks.uiuc.edu/Research/vmd/plugins/topotools/$>

After loading in VMD the coordinate file with autobonds off:
https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node140.html$>
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.

Giacomo

On Wed, Nov 24, 2021 at 3:56 PM Bennion, Brian <bennion1_at_llnl.gov<mailto:bennion1_at_llnl.gov>> 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