On Mon, Dec 16, 2013 at 2:42 AM, <ansu...@physics.iisc.ernet.in> wrote:

> 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.
You probably have missing atoms or are incorrectly choosing protonation
states for termini, but since you haven't shown us your command or the
screen output indicating your selections and any warnings from pdb2gmx, it
is hard to say.




Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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