[gmx-users] query regarding neutralisation of charge on protein

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 25 12:21:51 CET 2010

sonali dhindwal wrote:
> Hello All,
> I am trying to do MD on my modelled protein and when I ran pdb2gmx 
> command, it is showing that
> Total charge -12.000 e
> now I read in the tutorial that when there is a total charge, then we 
> have to neutralise that charge by adding ions, but in my case it is in 
> negative (what the output is showing). So what should I do ?

Why is a negatively-charged protein theoretically any different from a 
positively-charged one?  Instead of adding negative ions, add positive ones to 
compensate for the charge.  The same principle applies - the net charge of the 
system, once constructed, should be neutral.


> Please help
> Regards
> --
> Sonali Dhindwal
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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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