Generating Protein Structure Files (psf) in Avogadro?

General Discussion
1

Hello,

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.

See https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node23.html

Kind regards,
Sean

2

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.

3

It looks like there’s also some support for writing PSF files from the ProDy Python package developed by the Bahar group at Pitt.

4

Great, thank you very much!