Re: [AMBER] the problem of charge

From: Ben Roberts <>
Date: Sun, 29 Apr 2012 17:52:23 +1200

Hi Cao,

On 29/04/2012, at 1:03 PM, xiaojiong wrote:

> 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?

You should make the system neutral, especially if you intend to run calculations with PME long-range electrostatics.

I think that an overall charge of 5.6 is surprising anyway. You would be advised to look into your charge generation and see if you can find out why. A common mistake, though perhaps not what's happened in your case, is to put caps (such as the acetyl group, ACE, and the N-methylamino group, NME) on residues, and to compute the charges requiring an integral charge for the whole system but not necessarily for the individual residues that comprise it. The individual residues (including caps, which should be treated as separate residues) should also have integral charges.

Hope that helps,
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Received on Sat Apr 28 2012 - 23:00:03 PDT
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