[gmx-users] Metal-Protein interactions

Justin Lemkul jalemkul at vt.edu
Mon Dec 4 15:21:32 CET 2017

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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


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