I seem to have misread that part of the original post, and I don't have any Python experience; my apologies for that. I still think the best course of action when switching to a new RTF/PARAM file pair is to make a new PSF, whether it's with CHARMM or a NAMD related tool. For POPC and/or DOPC some atom names must be changed when adopting all36_lipid, but a simple 'sed' script based on the CHARMM stream file should suffice for most coordinate formats. Change the atom names in a coord file, make a new PSF, and the conversion is complete.


Rick Venable
computational chemist