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

errabah fatima ezzahra errabahf at yahoo.fr
Fri Jul 8 20:36:30 CEST 2011 

Hi All 


I am using course grained model where i have the whole glutamic acid as a sphere , and the other end is Lucine (hydrophobic) , do i need to still worry about capping the residue to evoid the negative charge in GLU from repelling other GLU .

Also is it possible to control the orientation of the peptides like to have them assembeled where it GLU LEU GLU LEU GLU LEU on one side of the  trminis and the other side trminiLEU GLU LEU GLU LEU GLU because i was thinking  that if it GLU GLU GLU than they will repel each other and that is my be causing the problem

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 17h03
Objet : Re: Re : Re : Re : Re : [gmx-users] Re: Hexamer problem/ The N and C termini of peptides



errabah fatima ezzahra wrote:
> Thank you so much for your help , my pdb file says that gen_seed = 473529 so i will change it to different numbers , but i saw online that  

Your .mdp file, you mean?

> some gen_seed = -1 and that to generate random seed is that correct ??

Yes, with -1 you will get a random number based on the process ID.

> also please  how i can control the starting initial states so that i can have starting from more one initial states??  tried looking it up on line but did not find that much information.
>  

If you generate different velocities, then that is a different state.  If you want to control what the velocities are (to some degree), then set gen_seed explicitly.  If you want to start from a different configuration, build a new starting structure.

-Justin

> Thank you so much
> 
> fatima ezahra
> 
> 
> 
> ------------------------------------------------------------------------
> *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 15h55
> *Objet :* Re: Re : Re : Re : [gmx-users] Re: Hexamer problem/ The N and C termini of peptides
> 
> 
> 
> errabah fatima ezzahra wrote:
>  > I am sorry to be asking you again but do you start with different velocities  by changing the temperature that will lead to change in velocities, i ma new to Gromacs so i dont know where to change he velocities, i checked the  mdp file and i didn't see any velocity
>  >
> 
> Keep the temperature the same and change gen_seed.
> 
> -Justin
> 
>  > thank you
>  >
>  > Fatima ezzahra
>  >
>  > ------------------------------------------------------------------------
>  > *De :* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  > *À :* Discussion list for GROMACS users <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>  > *Envoyé le :* Jeudi 7 Juillet 2011 14h55
>  > *Objet :* Re: Re : Re : [gmx-users] Re: Hexamer problem/ The N and C termini of peptides
>  >
>  >
>  >
>  > 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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> 
> -- ========================================
> 
> 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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> 

-- ========================================

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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