VMD-L Mailing List
From: Joyce Yang (yang624_at_uab.edu)
Date: Tue Sep 09 2014 - 10:38:00 CDT
I was trying to compare the conformation energy between the wildtype and
mutant. while i was breaking down the backbone and sidechain, I noticed
that there is a huge difference in the dihedral energy.
Out of curiosity, I did NAMD for the backbone between the initial structure
of the wildtype and mutant (used the vmd plugin to create point mutation).
The two structures have the exactly same backbone (RMSD = 0), but the
dihedral energy calculated by NAMD energy are different in over 100
Anyone has an explanation for this?