VMD-L Mailing List

From: Francesco Greco (francesco.greco_at_chimfarm.unipg.it)
Date: Sat Oct 24 2015 - 09:44:14 CDT

Hi everybody,

I've used HEME patches during last month to run MD simulations. In
particular I've used PHEM patch. I've read that when you treat HEME also
FHEM patch should be used with the first one. Is it true?
Now I need a 6 liganded HEME, that coordinate His and O2. I've seen n the
.rtf CHARMM files the possibilty to use PLO2 patch to obtain my goal. But
I've never used a three atom patch. How can I do in the AutoPSF Generator?
I've tried doing two PLO2 separate patches (O2-HEME; HEME-His) but in the
autopsf.psf I can't see the interaction between the iron and the His, just
the one with the gas molecule.

Sorry for the maybe-stupid question.

Francesco A. Greco

PhD Student - Computational medicinal chemistry
Department of Pharmaceutical Sciences
University of Perugia