VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Mar 27 2013 - 08:24:31 CDT

On Mar 27, 2013, at 3:34 AM, Francesco Pietra wrote:

> 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.

Just because a molecule is lipophilic doesn't meant that it does not form any favorable interactions with water. I suggest you run the calculations and see if a minimum interaction energy and distance are found for either orientation of water.

> 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.
>

The algorithm behind the autoselection of H-bond donor and/or acceptor is admittedly quite simplistic, and was designed to be used as a starting point for use with more common organics. Users should always apply their chemical knowledge of their specific molecule to assess these assignments. That said, for reasonably sized systems, the water interaction calculation is quite fast. A mis-assigned h-bond donor/acceptor will result in an abnormally terminated calculation (does not converge) or unrealistic water position (generally very far away), so there's not a huge risk associated with mis-assignment--just exclude these target data from the optimization.

> 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