CCL: Problems about AMBER

["David A. Case" <case..scripps.edu>]

 Sent to CCL by: "David A. Case" [case(_)scripps.edu]
 On Wed, Jun 13, 2007, littlecan p9894105%x%mail.ncku.edu.tw wrote:
 >
 > Recently, I started using AMBER and have encountered problems regarding van
 > der waals energy calculation.
 It is far better to submit Amber-related questions to the Amber mailing list;
 see http://amber.scripps.edu for information on how to subscribe
 and post.
 > We are not sure about either our calculation is incorrect or it is
 > reasonable to have positive van der waals energy in those cases.
 There is nothing intrinsically suprising about have a postive value here.
 >
 > 2.                  In the 1995 paper by Cornell et al., the scale factor
 of
 > 1/2.0 is recommended for reducing the 1-4 VDW interactions as used
 > previously by Weiner et al. (lines 6 to 8 from the bottom of the right-hand
 > column in page 5183). Is our interpretation correct?
 This sounds correct to me.
 ...regards...dave case