[gmx-users] Metal-Protein interactions

[Justin Lemkul]

On 12/4/17 6:53 AM, RAHUL SURESH wrote:
> Dear Justin
>
> I have manually added Cu ion to the protein structure. the total charge of
> the system is -0.99999. How do I make sure that  gromacs is considering Cu
> in +2 state only?

pdb2gmx writes a topology based on whatever you tell it. If you 
specified an ion with a +2 charge, that's what's used. Verify that in 
the pdb2gmx screen output (if it was a separate chain, it should say) or 
just look in your topology.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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