VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Aug 13 2007 - 17:35:01 CDT

Hi Thomas,
this is certainly possible to do; there are a couple of different
possibilities. Do you need this psf you want to create for visualization
or simulation? If you only need to visualize things, you can just use
the $sel writepsf command; this will write atoms and bonds, but not
angles or dihedrals (so it isn't appropriate for simulation).

If you need a "real" psf you'll probably need to use psfgen manually. If
you're deleting some sections of protein or certain atoms from complete
residues, autopsf is probably adding in termini where you've made gaps.
It would help if you could be more specific about what you've deleted.
If your modified pdbs have *incomplete* residues, then psfgen will
complete them based on standard topologies.

Also, for writing dcds, you should try the "animate write" command...

Peter