[gmx-users] Re: Reasonable for drug molecule using united atom topology?

[Anton Feenstra]

Ing. Vojte(ch Spiwok wrote:

> I think that higher is a "protein-like" character of the drug, better is performance of
> united-atom model. I would expect it to performe well on peptide and peptidomimetic
> drugs. United-atom force filed would in my opinion fail if there is a significant role of
> cation-pi, CH-pi etc. interaction that can be (somehow) treated in all-atom model.

The united atom forcefields I know, *do* contain all polar hydrogens (obviously)
as well as 'aromatic' hydrogens, most notably on aromatic rings. On unsaturated
aliphatic chains they are usually not included, but they could easily be added
in analogous manner to the aromatic hydrogens. That would save you a lot of work
(topology writing and parameter definition & optimization) for the remaining
non-polar, saturated hydrogens (which are the majority, usually).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|