> 2) I have some small molecules with F and Br and it seems that the GB radii
> and screening parameters don't exist. Does anyone have these or know where I
> can find them? If not where should I start if I want to develop these
> myself.
F and Br's GB radii and overlap parameters have not yet been optimized for
molecular dynamics simulations. For rough approximations or
optimization starting points, you could check out values in Hawkins et
al., J. Phys. Chem. 100:19824-19839, 1996. To add GB parameters for new
atoms in amber 6, simply add to ~line #623
else if( atsymb.eq.'B' ) then
x(L96-1+i) = 0.96d0
x(L97-1+i) = 1.40d0
where the first variable is the screening parameter and the second is the
GB radius.
vickie
The Scripps Research Institute
10550 North Torrey Pines Road, TPC-15
La Jolla, CA 92037
TEL: (858)784-9788
FAX: (858)784-8896
Received on Mon Jun 12 2000 - 10:05:46 PDT
