[gmx-users] specbond definition

Justin Lemkul jalemkul at vt.edu
Wed Jan 16 13:22:20 CET 2013

On 1/16/13 6:54 AM, Serdar Durdagi, PhD wrote:
> 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

If the isopeptide bond should be present, it must be defined as such.  Bonds 
won't break or form during MD, so if you have ionized groups and no bond, then 
none will ever emerge.  You need to define the state you wish to simulate at the 
outset of the run.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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