Thank you Bill. 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? Or what other methods to
consider? Thanks.
Lan
Quoting Bill Ross <ross.cgl.ucsf.edu>:
> > 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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Received on Wed Feb 18 2004 - 19:53:01 PST
