I am trying to generate protein structure files (psf) for use in VMD, but the automatic psf builder (Extensions → Modeling → Automatic psf builder) has been crashing on me. Does Avogadro currently have the ability to generate psf’s? If not, that would be a nice feature.
Some parts of that wouldn’t be bad, but assigning CHARMM atom types would be the big stumbling block. (Assigning correct donors, acceptors are probably okay, but cross-terms would also be hard.)
My suggestion would be to check out the https://charmm-gui.org website, which should presumably generate PSF files for you.
It looks like there’s also some support for writing PSF files from the ProDy Python package developed by the Bahar group at Pitt.
Great, thank you very much!