Hi,
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
Serdar
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