VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Mon Oct 30 2023 - 07:22:18 CDT

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>-----
>
>