[gmx-users] specbond definition

Serdar Durdagi, PhD durdagis at ucalgary.ca
Wed Jan 16 12:54:20 CET 2013

In my system, I have a special bond (isopeptide bond, i.e., a bond 
between amino group of Lys and the carboxyl terminus of another 
protein). Before the simulation, is this bond should be formed or both 
LYS (which is defined with different residue name, e.g., LYX) and 
carboxyl terminus of another protein (which is Gly in my system; defined 
as GLX) should be in their standard forms (-NH3+, and -COO-, 
respectively). I defined this bond in specbond.dat as:

LYX     NZ      1       GLX     C       1       0.135    LYS2 GLY2


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