[gmx-users] Zn moves away from protein - ligand complex

HongTham hongtham0709 at gmail.com
Mon Apr 18 13:40:21 CEST 2016

Hello Gromacs users,
I'm running a Zn bound protein - ligand complex simulation. I solvated
whole system in a dodecahedron box. I also meet the problems with boundary
effects. I try to use the gmx trjconv with option -pbc mol -ur compact
-center to fix the problem. However, it doesn't work. The protein and
ligand was centered to the water box, but not Zn ion.
In some frame, Zn stay in the active site, sometime, it appear out site of
the active site. I use VMD and display the system with many box (not only
one unit), and see ZN till stay in the active site, but that is Zn of
neighbor box, not the current box. its Zn ion now is stay in the active
site of another box.
I also tried with many option (cluster, nojump, -fit rot+trans) or change
the selection of centering but they all useless. The -pbc nojump seems to
be fine , it makes the protein + ligand + Zn stay together, but the water
molecules are definitely distracted. It is difficult for me to calculate
the water molecules within 0.5 to 10 nm of Zn and ligand.
Anyone has been same situation with me? Would anyone give me a suggestion
to fix that problem.
Thank you so much.
Best regards,

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