On 9/24/12 3:01 AM, Arunima Kumar wrote:
Dear Sir
I have performed MD simulation of a protein and the system uses 2
sodium and 19256 SO42 as charge neutralization system. I am unable to
understand why my protein uses this much of negative ions. Negative ions
used in such a high quantity might genertae a highly negative system.
Should i proceed further or check my protein in terms of amino acids before
proceeding to next step.
It seems highly unlikely to me that any protein has a net charge of nearly
+40000. I would check carefully before proceeding.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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