VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Fri Nov 03 2023 - 07:32:57 CDT

W dniu 2.11.2023 o 18:21, Diego Gomes pisze:
> Thanks to Yupeng & Hale the issue has been found and addressed in the
> CVS source.

Thank you, now it works!
Paweł

> To fix it in your installed version, please change line 2692 of
> *molefacture_internals.tcl *
>
> from
> *set notcgenfftopo 1
> *
> to
> *set notcgenfftopo 0*
>
>  (see attached image)
>
> You may find molefacture_internals.tcl at
>
> MacOS
> /Applications/VMD\
> 1.9.4a57-arm64-Rev12.app/Contents/vmd/plugins/noarch/tcl/molefacture2.0/molefacture_internals.tcl
> <https://urldefense.com/v3/__http://1.9.4a57-arm64-Rev12.app/Contents/vmd/plugins/noarch/tcl/molefacture2.0/molefacture_internals.tcl__;!!DZ3fjg!-A2q2SeSqqppZEWAf5OLCNu55t5nmLoAccOlM5zRBHUn4xR8D57RRPej91HV_T9wW5hnRMPkPzuNpFufst3Tx4wIiAWvGprf$ >
>
>
> Linux
>
> vmd_install_path/lib/vmd/plugins/noarch/tcl/molefacture2.0/molefacture_internals.tcl
>
>
>
> Please let us know if you find any other issues.
>
>
> Friendly regards,
>
> Diego.
>
>
> Screenshot 2023-11-02 at 12.12.32 PM.png
>
>
>
> On Mon, Oct 30, 2023 at 12:58 PM Jirui Yang <jirui_at_hawaii.edu> wrote:
>
> 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>-----
> >
> >
>
>
>
> --
> Diego Enry B. Gomes, PhD
> Department of Physics at Auburn University &
> NIH Center for Macromolecular Modeling and Visualization
> Leach Science Center - Ste. 3182 - Auburn, AL
> dgomes_at_auburn.edu