VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Mar 27 2013 - 08:00:01 CDT

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