Hi,
if you have +1->+1 and +2->+2 transformations that work well, and +2->+1
ones that dont, do you see some difference in your +2 vs. +1 starting
structures? And if yes, were does that come from and is that change
showing up during your TI runs?
The rotamer change (or lack of it) of a single charged amino acid may
introduce as much error as your mentioned and may not occur during an MD
simulation.
Of course, I'm only speculating right now and if all your starting
structures come from the same X-ray, disregard this comment...
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Jan 28 2010 - 08:00:03 PST
