From: Anna Petroff (
Date: Thu Mar 15 2018 - 10:33:15 CDT


I'm seeking recommendations on how to identify non-heme coordinations
between iron and His in VMD/NAMD. From what I've read, there are some nice
patch options for heme coordination, but I haven't found one specific to
non-heme coordination. Is there a best-practice way to handle this

My protein of interest has a diiron active site. One of the irons is
coordinated with five histidine residues (all HSE). The other iron is
coordinated with four histidines (also all HSE), as well as an interaction
with a glutamine residue that is mediated by a water molecule.

I would like to set these coordinations in NAMD2, possibly through a
combination of patches. If you have experience related to this type of
problem, I'd really appreciate your thoughts.

Thanks for your time,