VMD-L Mailing List

From: Jirui Yang (jirui_at_hawaii.edu)
Date: Mon Oct 30 2023 - 12:20:33 CDT

I still need to regenerate your problem. However, in my most recent
research using VMD, it has appeared that some bonds will disappear after
running calculations. We thought it was a bug at first. Please keep
me updated on this issue.
Respectfully
Jirui

On Mon, Oct 30, 2023 at 3:07 AM Pawel Kedzierski <
pawel.kedzierski_at_pwr.edu.pl> wrote:

> My apology for the double posting, but I've just realized that my vmd
> was not the most recent one and I have confirmed, that the problem
> persists in 1.9.4a57 for Linux
> Also, at the time of saving PSF and PDB files from Molefacture I
> answered "No" to the question, whether to download the topology from the
> CGenFF server.
> With regards,
> Paweł Kędzierski
>
> W dniu 30.10.2023 o 08:54, Paweł Kędzierski pisze:
> > Dear All,
> >
> > Since several years I use Molefacture & FFTK on my molecular modeling
> > classes. This year I have switched to using Molefacture 2 and I have
> > observed, that the angles and dihedrals are not generated from the
> > bonds and therefore missing in the saved the PSF file. Perhaps I am
> > missing something, but I don't see any option to generate them on
> > request. On the other hand, Molefacture 1.0 available with vmd1.9.4a8
> > saved the PSF file with complete topology information.
> >
> > To reproduce the problem, you may save the example below as a
> > h2o2.mol2 file, load it into VMD, open
> > Extensions->Modeling->Molefacture, create a new working molecule in
> > Molefacture using File->New molecule->From selection (using the
> > selection "all"), and then save with File->Write PSF and PDB files. In
> > the PSF file, there are 0 angles and 0 dihedrals. The same happens
> > with the option Build->Topology & Parameters->Export to FFTK.
> > This was tested using vmd1.9.4a55 on Linux Debian 12.
> > How can I fix this, to create the PSF file with complete topology,
> > usable with FFTK?
> > With regards,
> > Paweł Kędzierski
> >
> > ----<h2o2.mol2 file contents----
> > @<TRIPOS>MOLECULE
> > *****
> > 4 3 0 0 0
> > SMALL
> > GASTEIGER
> >
> > @<TRIPOS>ATOM
> > 1 O 0.1046 -0.1116 -0.5641 O.3 1 UNL1
> > -0.2528
> > 2 O 0.5297 -0.9231 0.5641 O.3 1 UNL1
> > -0.2528
> > 3 H -0.6326 0.3369 -0.1076 H 1 UNL1
> > 0.2528
> > 4 H -0.0658 -1.6768 0.3903 H 1 UNL1
> > 0.2528
> > @<TRIPOS>BOND
> > 1 1 2 1
> > 2 1 3 1
> > 3 2 4 1
> > ----<cut above this line>-----
> >
> >
>