VMD-L Mailing List

From: Zack Scholl (zack.scholl_at_gmail.com)
Date: Thu Apr 26 2012 - 19:57:48 CDT

Hi everyone,

I am currently trying to generate a PSF file for PDB 2X5P which contains a
isopeptide bond between residues 31 and 117. However, each time I generate
a PSF file, using psfgen and AMBER99ff or the internal VMD psfgenerator
with the built-in CHARMM ff, the isopeptide bond disappears. Is there
something i need to do to do the force field or the pdb file for the
isopeptide bond to be recognized? I haven't found much information about
this so I was wondering if anyone has run into this or has any ideas!
Thanks a lot!!

Sincerely,
Zack