[gmx-users] Adding Ions

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 13 19:05:58 CEST 2011

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 

>  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 


> 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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