[AMBER] the problem of charge

From: xiaojiong <xiaojiong.zju.edu.cn>
Date: Sun, 29 Apr 2012 09:03:08 +0800

Dear sir/madam,

I am a user of AMBER in China. My system is a protein complex with phospholipid membranes. The particial charge of DPPC is calculated in GAUSSIAN. The charge of my ligand is calculated in AMBER with AM1.
I load the pdb file into tleap and find the whole charge of my system is +5.6. So I add 6 Cl- which change the charge to -0.4 rather than zero. I wonder why the total charge is not zero. So My question is:

Whether the charge equaling -0.4 be resonable in MD simulation? If not, how should I make the system neutral?
Thanks for your time!

Cao Yang,
Zhejiang University, China
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Received on Sat Apr 28 2012 - 18:30:04 PDT
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