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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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