From: Francesco Pietra (
Date: Wed Mar 27 2013 - 03:34:30 CDT

In addition, I wonder whether treating NO as a H-bond acceptor base is
sound at all. NO lipophilicity is comparable to that of noble gases
and dinitrogen. In FFTK, autoselection indicates both atoms of NO as
H-bond acceptors. Even though the Water Interaction module will run, I
wonder whether chemistry will be taken into account.


francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <>
Date: Wed, Mar 27, 2013 at 8:21 AM
Subject: vmd-l: FFTK Atom types
To:, NAMD <>

I am looking for a comprehensive list of atom types for charmm27 ff to
use with namd/vmd/fftk. I was only able to find partial lists, such as
at <>

With inorganic molecules, such as NO, the selection of atom types is
not obvious (for me). With NO I placed in FFTK atom type NO2 for
nitrogen and atom type OM for oxygen (tentatively). H-F optimization
was carried out but I am still in doubt.


francesco pietra