[gmx-users] Adding Ions
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 13 19:48:05 CEST 2011
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
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.
> *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:
> > 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.
> > 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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