From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Mar 27 2013 - 10:54:21 CDT

Thanks a lot for these references. I knew that prof Shulten was
involved with NO but I thought that he followed Karplus' school, so
that I skipped his work on NO. Karplus' school - as you may know - has
made the problem of NO extremely complex, with three-pole or multipole
models, and Morse instead of harmonic potential. Multipole requires
special routines, now available with CHARMM code (which I don't have,
and, using CUDA acceleration, I am not interested in), but, as far as
I know, it was never implemented on NAMD (although probably feasible).

At any event, I'll not pick up directly Prof Shulten's NO
parametrization. It is an occasion to learn to use the FFTK plugin and
see were it brings with NO. Nonetheless, the doubts I posted about a
model of NO interacting with both N and O atoms with water hydrogen
atoms is not what a chemist can digest easily.

Have a nice day

francesco pietra

On Wed, Mar 27, 2013 at 2:00 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> You're right to be worried about the atom type, as the LJ parameters will likely be important for NO. All I can suggest though is to look to the following publications:
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805761/
>
> http://www.ncbi.nlm.nih.gov/pubmed/16751246
>
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Francesco Pietra
> Sent: Wednesday, March 27, 2013 4:35 AM
> To: vmd-l_at_ks.uiuc.edu; namd_at_ks.uiuc.edu
> Subject: Fwd: vmd-l: FFTK Atom types
>
> 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
>