VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Mon Oct 30 2023 - 02:54:26 CDT

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>-----