AMBER Archive (2004)

Subject: Re: AMBER: Close contact warnings

From: Bill Ross (
Date: Wed Feb 18 2004 - 12:20:38 CST

> The type of H54 is HO 'hydroxyl group' within parm99.
> And in my molecule it is attached to the oxygen which is
> part of the sulfate group, -SO3H. I have
> introduced the atom type for the S atom. And O41 is OS in parm99 too. The
> positions of H54 and O41 are like this R-O41-SO3H54. Both of the parms of H54
> and O41 are from Parm99. Do I need to modify the VDW parm? Thanks

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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