[gmx-users] fractional charge

ansuman at physics.iisc.ernet.in ansuman at physics.iisc.ernet.in
Mon Dec 16 09:01:07 CET 2013

Dear gromacs users,

I have run pdb2gmx for dimer with one MG ion in each chain.

1) If I run without Mg the total charge is -8.00 (-4.00 in each chain)
2) If I run with Mg the total charge becomes :

a) -4.00 for A chain and +2.00 for Mg in A chain, total -2.00
b) -4.129 for B chain and +2.00 for Mg in B chain, total -2.129

Why does this fractional charge arise? I checked the PDB and found no
covalent bond with Mg in any of the chains.

3) Then I removed Mg from B chain and found:

a) -4.00(a chain) + 2.00 (Mg of A)
b) -4.129(b chain)

Please suggest.


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