AMBER Archive (2003)

Subject: SSBonds and charge problems

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Fri Apr 11 2003 - 14:54:23 CDT


Hi
I am experiencing some problems with my disulfide bonds. When I start
out at 0.00 time, I have disulfide bonds(CYX), but after just 125 fs
they break and separate. Why is this?

Another problem I have is that in leap when I load my protein, it tells
me that it has zero unperturbed/perturbed charges without any addition
of counter ions or water. Why is this?

Thanks, Steve

-- 
  Steve A. Seibold , Ph.D.
  22A  Chemistry Building
  Michigan State University,
  East Lansing, MI 48824
  517-355-9715;ext.258