From: Brianna McIntosh (
Date: Thu Jul 30 2015 - 17:32:56 CDT


 I have been trying to generate the psf file for a pdb of a protein
that has a bimane probe linked to a cysteine. It appears that VMD's
Automatic PSF Builder is ignoring the atoms of the bimane while
generating the psf for the rest of the residues.

Is there a way to generate the psf for all of the atoms such that
simulations can be run taking the dynamics of the probe into account?