VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 26 2021 - 19:25:44 CST

There also is:
https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/
which is *really* old, so it may need a few tweaks. I remember using it a
long time (10+ years) ago.
The major trick with this is to capture the preprocessed intermediate
gromacs topology file when running grompp, since the script does not do
pre-processing.

On Fri, Nov 26, 2021 at 8:13 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> 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!riPXq_La_AMjZpE6FeYSOmlhnQlEDD9LrMbovomO4o4C7LJWVr1ODrXeF_Bj8BTBMg$
> <https://urldefense.com/v3/__https://github.com/jvermaas/vmd-tprreader__;!!DZ3fjg!rOr5uRQ-B2SQp6Jhf9JUywdQTOCdee740CSdyelOz2mTPjlevyRBYuNGnOlPAVYedw$>
>
>
>
> -Josh
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Giacomo Fiorin <
> giacomo.fiorin_at_gmail.com>
> *Date: *Wednesday, November 24, 2021 at 6:46 PM
> *To: *"Bennion, Brian" <bennion1_at_llnl.gov>
> *Cc: *"vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> *Subject: *Re: vmd-l: support for gromacs topology files
>
>
>
> Hi Brian, I'm not sure if there is a pre-cooked tool, but MDAnalysis does
> read TPR files:
>
> https://urldefense.com/v3/__https://userguide.mdanalysis.org/1.1.1/formats/reference/tpr.html__;!!DZ3fjg!riPXq_La_AMjZpE6FeYSOmlhnQlEDD9LrMbovomO4o4C7LJWVr1ODrXeF_Cwo-gV7w$
> <https://urldefense.com/v3/__https:/userguide.mdanalysis.org/1.1.1/formats/reference/tpr.html__;!!DZ3fjg!sF8fHozb7Go25G7u8XSD0Z7Q6rWB1ttRInyGFW7ayJjfWnK1UBMVSbJd_OWVsH2bJQ$>
> including bond information.
>
>
>
> From there, with a bit of Python code you can write out a Tcl script that
> re-creates all correct bonds in VMD. Use e.g. TopoTools for this purpose:
>
> https://www.ks.uiuc.edu/Research/vmd/plugins/topotools/
> <https://urldefense.com/v3/__https:/www.ks.uiuc.edu/Research/vmd/plugins/topotools/__;!!HXCxUKc!lZz4cv1z3kee0sFJmydp2kH7Fvoh_E6MGreEIu2fpyAoUEeDlxwTicmVpS3fOFE$>
>
>
>
> After loading in VMD the coordinate file with autobonds off:
>
> https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node140.html
> <https://urldefense.com/v3/__https:/www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node140.html__;!!HXCxUKc!lZz4cv1z3kee0sFJmydp2kH7Fvoh_E6MGreEIu2fpyAoUEeDlxwTicmVchjz99U$>
>
> 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> 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
>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!riPXq_La_AMjZpE6FeYSOmlhnQlEDD9LrMbovomO4o4C7LJWVr1ODrXeF_DpbsBhtw$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.