[gmx-users] Adding Ions
errabah fatima ezzahra
errabahf at yahoo.fr
Wed Jul 13 19:45:01 CEST 2011
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.grofile 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
[ system ]
[ molecules ]
; Compound #mols
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.
> thank you so much for your help
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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