VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
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.

thanks

francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Mar 27, 2013 at 8:21 AM
Subject: vmd-l: FFTK Atom types
To: vmd-l_at_ks.uiuc.edu, NAMD <namd-l_at_ks.uiuc.edu>

Hello:
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 <http://www.chem.cmu.edu/courses/09-560/docs/msi/ffbsim/B_AtomTypes.html>

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.

Thanks

francesco pietra