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

Ing. Vojtěch Spiwok Vojtech.Spiwok at vscht.cz
Wed Jan 21 10:08:01 CET 2004

> 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
> 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
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

Vojtech Spiwok
ICT Prague

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