errabah fatima ezzahra wrote:
*
hello
Does anybody knows why The N and C termini of peptides can be
neutralized before running simulation of peptides ?? i read this some
where in a research paper , they dont say why but they do that using
acetyl amine groops. Probably to evoid the repulsive interactions
between the end of the peptides , please correct if i am wrong as my
chemistry is not good, my one trimer is made of 3 peptides that ends
with GLU LEU LEU and the other trimer ends with is LEU GLU LEU , should
i worry about neutralizing the c and N termini
Capping groups can be added to termini using different software programs. There
is no utility in Gromacs to do so. Once built, choose 'None' for the termini
when running pdb2gmx to build a normal peptide bond between the terminal
residue(s) and capping group(s).
Such groups are often added (1) if artificial terminal attraction or repulsion
should be avoided or (2) if the modeled peptide is a segment of a longer
polypeptide or protein, in which case such integral charges are an incorrect
representation of reality.
Also what the important of running 20 simulations of the same 6
peptides ???. is that to compare the 20 simulation results and see ****
which give better simulation sorry if my question are something i should
know. i am trying to find how to get six peptides to self assemble to a
hexamer . i will really appreciate your answers.
Running multiple simulations of a given configuration (using different starting
velocities) gives better sampling. You can't conclude anything from a single
trajectory. Just as you wouldn't run a single experiment on the bench and call
it conclusive, so too is it true of simulations - if you run just one
simulation, how do you know you're not seeing the one outlier in the data set?
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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