[gmx-users] energy minimization and ions

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Wed Apr 28 14:50:01 CEST 2004

Hi all,

I want to energy minimize a structure (two proteins + 4 ligands) in a
water box (dodecahedron). The total charge is not 0. what should I do
- add the ions I need to avoid this charge.
- add negative ions to compensate the positive charges (Asn, Gln in the
protein and positive charges in the ligands) and positive ions to
compensate negative charges (Glu, Asp in the protein and ligands), so
the total charge will be 0.

Thanks in advance,


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