[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 

#include "martini_v2.1.itp"
#include "1pef.itp"
#include "martini_v2.0_ions.itp"
[ system ]

; Name


[ molecules ]

; Compound        #mols

Protein             6

W                   3551


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
> FZ

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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