AMBER Archive (2004)

Subject: Re: AMBER: Close contact warnings

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Feb 18 2004 - 13:29:19 CST

> Is it possible to modify some VDW parms to avoid the HO and OS
> or some other atoms to sit on top of each other?

Yes. Then you would have to think of the other uses of the existing
types and write up how your new ff differed from the standard one.

> Or what other methods to consider? Thanks.

See my answer that you quoted (create new vdw or use existing atom
type):

> > HO has no vdw. Given that hydroxyls in the Cornell et al. ff
> > are modeled as vdw-less HO's within the radius of the OH, perhaps
> > it is worth considering adding a sulfate O type with an even larger
> > radius, perhaps the same as OW or larger. Here are the radii of the
> > oxygen types:
> >
> > O 1.6612 0.2100 OPLS
> > O2 1.6612 0.2100 OPLS
> > OW 1.7683 0.1520 TIP3P water model
> > OH 1.7210 0.2104 OPLS
> > OS 1.6837 0.1700 OPLS ether
> >
> > Such an approach would keep in the spirit of the Cornell et al. ff;
> > alternatively one could think of using an H type with a non-0 vdw.
> >
> > Bill Ross
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