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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