Re: GB parameters

From: Vickie Tsui <>
Date: Mon 12 Jun 2000 10:05:46 -0700 (PDT)

> 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.


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Received on Mon Jun 12 2000 - 10:05:46 PDT
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