[gmx-users] Re: Hexamer problem/ The N and C termini of peptides

[errabah fatima ezzahra]

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 <jalemkul at vt.edu>
À : Discussion list for GROMACS users <gmx-users at gromacs.org>
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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