[gmx-users] Metal-Protein interactions
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.
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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