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.
-Justin
Please help
Regards
--
Sonali Dhindwal
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--
========================================
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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