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

Eric Jakobsson jake at ncsa.uiuc.edu
Tue Jan 27 02:24:01 CET 2004

Rough rule of thumb: Linear hydrocarbons are o.k. for all atom but cyclic 
hydrocarbons are not.  Evidence:  You can replicate properties of liquid 
linear hydrocarbons with united atoms but can't do it for benzene.  For 
benzene you must use all atom.  Basic reason is as Vojtech says: you can't 
describe cation-pi interactions with united atom, so where they are 
important, united atom does not work.  Another way of putting it: united 
atom vdw does o.k. with dipole-dipole via sixth-power attractive term, but 
can not replicate important quadrupole interaction such as generated by a 
ring compound.


At 10:07 AM 1/21/2004 +0100, you wrote:
> > 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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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical Information Science 
and Technology Initiative Consortium, but maintaining my research lab at 
Illinois by periodic commuting.  My usual schedule is four days a week at 
NIH and three days a week at Illinois.)

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