[gmx-users] Adding Ions

[Justin A. Lemkul]

errabah fatima ezzahra wrote:
> i added the NA using the genion 
> 
>     *
> 
>       genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the NA to the topology file , subtracted the water number by 6.  tail waterbox_ions.gro file have  this 
> 
>  3567W        W 3789   1.256   3.600   3.784
>  3568W        W 3790   2.491   6.539   2.341
>  3569W        W 3791   2.432   6.349   3.116
>  3570NA      NA 3792   2.677   4.903   3.617
>  3571NA      NA 3793   0.466   3.245   4.787
>  3572NA      NA 3794   6.028   4.147   2.550
>  3573NA      NA 3795   3.201   1.027   5.879
>  3574NA      NA 3796   1.677   1.849   6.641
>  3575NA      NA 3797   5.729   5.645   7.089
> and the topology file
> #include "martini_v2.1.itp"
> #include "1pef.itp"
> #include "martini_v2.0_ions.itp"
> [ system ]
> 
> ; Name
> 
> PEPTIDE F
> 
> [ molecules ]
> 
> ; Compound        #mols
> 
> Protein             6
> 
> W                   3551
> 
> NA+6
> 

This looks fine.  There are other things I suggested you look at; you haven't 
ruled out that something else went wrong along the way or that your peptide 
doesn't have the net charge you think it does.

-Justin

> ------------------------------------------------------------------------
> *De :* Justin A. Lemkul <jalemkul at vt.edu>
> *À :* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Envoyé le :* Mercredi 13 Juillet 2011 13h05
> *Objet :* Re: [gmx-users] Adding Ions
> 
> 
> 
> errabah fatima ezzahra wrote:
>  >
>  > Hi All,
>  >
>  >
>  > I have a peptide that has three positive charged amino acids  (LYS) 
> and four negative charged amino acids (GLU) consequently it is a 
> negative peptide. is that right
> 
> Assuming typical protonation states, and further assuming that there are 
> no other unbalanced charges in the peptides, yes.
> 
>  > when i run gromacs simualtion grompp DOES NOT gave a warning: System 
> has non-zero total charge: -6 ( i have six peptides)
>  >
> 
> Then you do not have what you think you do.  Look at the topology to see 
> what the net charge on each peptide is and determine whether or not this 
> is what you want.
> 
>  >  i tried neutralising the system, since that the peptides have an 
> extra -1 charge per peptide.
>  >
>  > however when i did add 6 NA to the system , after running the enrgy 
> minimization there was an error that System has non-zero total charge: 
> -6.000000e+00
>  >
>  > so i dont understand how by adding 6 positive ions that cause the 
> negative charge??
>  >
> 
> It can't.  You've probably confused which files you're using or are 
> misreading some output somewhere along the way.  Adding six positives 
> cannot give six negatives.
> 
> -Justin
> 
>  > thank you so much for your help
>  >
>  > FZ
>  >
>  > 
> 
> -- ========================================
> 
> 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

========================================