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

[Ing. Vojtěch Spiwok]

> Hi,  everyone:
>
> Has anyone done the drug related analysis using united atom topology for
> drug molecule? Is that all right for using united atom topology rather
than
> using all atom topology for drug molecule? has someone published paper
> related to using united atom topology of drug molecule and get reasonable
> results? I just want to make sure whether there are published reference to
> support to use united atom topology of drug molecule for the study.
>
> Thanks,
>
> Yuhua
>
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.

Vojtech Spiwok
ICT Prague