Homa Azizian wrote:
Hi
there is total charge of 0.08 on the protein, Is it correct to add 1 CL- or
it should better ignore this?
You should absolutely NOT ignore this problem. You have a fractional charge of
non-negligible magnitude. Did you use -missing with pdb2gmx? If so, you are
probably not accounting for some atom that should otherwise be present.
As it stands, your system is non-realistic.
-Justin
--
Tehran University of Medical Sciences
www.tums.ac.ir
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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