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
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.
Thank you
fatima ezzahra
De : Justin A. Lemkul <[email protected]>
À : Discussion list for GROMACS users <[email protected]>
Envoyé le : Jeudi 7 Juillet 2011 9h33
Objet : Re: Re : [gmx-users] Re: Hexamer problem/ high and low salt solutions.
errabah fatima ezzahra wrote:
> Hi
everybody
>
> i did Again run the simulation for 2000ns and the proteins were just moving
>every were , they were forming the two rimers but not for along time like in
>the simulation with the 200ns and 20 ns.
>
> Justin : i did check the periodic boundary using VMD and it does not to seem
> to be the case. thank you
>
> so I am thinking about running the simulation in diferrent solutions like low
> salt , high salt and organic solvent ... I am new to gromacs and i only used
> water to solvate the system and wondering if using different pH solution and
> different salt concentration solution is something possible to do . i did
> some research and found out that you can add ions like NA+ and CL_ but i was
> wondering if anybody does have an idea of some solution that already have a
> pH known or solutions with high salt concentaration that i can use instead of
> water when solvaiting the system.
>
You can
apply basically any conditions you wish. genion will allow you to add any
number of ions (and there are more than just Na+ and Cl-) that you wish. Simple
stoichiometry and unit conversion can be done to calculate however many ions
you may need to add.
pH is a different matter. In classical simulations, a concept like pH does not
directly apply, since protons cannot be exchanged. You can set different
protonation states for titratable residues when running pdb2gmx. See the list
in the manual and/or pdb2gmx -h.
If you want to solvate with something other than water, read this:
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
-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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