From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Thu Nov 25 2021 - 06:23:34 CST

Hello Brian,

Did you have a chance to look at https://urldefense.com/v3/__http://cgmartini.nl/index.php/__;!!DZ3fjg!ppuOiL97rbGrfH4CJxG0BOjRBEzDTQCTc2xd0bx1315rg4Ygnc_BK2Qt6a6vXHMpCQ$ <https://urldefense.com/v3/__http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/cgviz-gmx5__;!!DZ3fjg!ppuOiL97rbGrfH4CJxG0BOjRBEzDTQCTc2xd0bx1315rg4Ygnc_BK2Qt6a7bjP8_-g$ >tutorials-<https://urldefense.com/v3/__http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/cgviz-gmx5__;!!DZ3fjg!ppuOiL97rbGrfH4CJxG0BOjRBEzDTQCTc2xd0bx1315rg4Ygnc_BK2Qt6a7bjP8_-g$ >general-<https://urldefense.com/v3/__http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/cgviz-gmx5__;!!DZ3fjg!ppuOiL97rbGrfH4CJxG0BOjRBEzDTQCTc2xd0bx1315rg4Ygnc_BK2Qt6a7bjP8_-g$ >introduction-gmx5<https://urldefense.com/v3/__http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/cgviz-gmx5__;!!DZ3fjg!ppuOiL97rbGrfH4CJxG0BOjRBEzDTQCTc2xd0bx1315rg4Ygnc_BK2Qt6a7bjP8_-g$ >/<https://urldefense.com/v3/__http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/cgviz-gmx5__;!!DZ3fjg!ppuOiL97rbGrfH4CJxG0BOjRBEzDTQCTc2xd0bx1315rg4Ygnc_BK2Qt6a7bjP8_-g$ >cgviz-gmx5<https://urldefense.com/v3/__http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/cgviz-gmx5__;!!DZ3fjg!ppuOiL97rbGrfH4CJxG0BOjRBEzDTQCTc2xd0bx1315rg4Ygnc_BK2Qt6a7bjP8_-g$ >?<https://urldefense.com/v3/__http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/cgviz-gmx5__;!!DZ3fjg!ppuOiL97rbGrfH4CJxG0BOjRBEzDTQCTc2xd0bx1315rg4Ygnc_BK2Qt6a7bjP8_-g$ >

I follow this for visualizing Gromacs-compatible MARTINI CG structures in VMD.

Regards,
Raman

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Thursday, November 25, 2021 4:17:45 AM
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!ppuOiL97rbGrfH4CJxG0BOjRBEzDTQCTc2xd0bx1315rg4Ygnc_BK2Qt6a6BS99Tjw$ <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