you are correct that you must include the water as part of the same
molecule (as you appear to have already done for Zn). I assume that
protein_ion_A.itp contains only one [ moleculetypes ] section that has
the protein and also the zinc. Take a look at how Zn has been included
there. Repeat this procedure to include the water that you want to be
bonded. Then modify your coordinate file accordingly. You can get
water parameters from gromacs-3.3.1/share/gromacs/top/tip3p.itp (or
sub the name of your favourite water model).
Note that this is intended as my best idea about how to go about doing
exactly what you have asked. I have no idea how this is going to
affect things like a temperature group that contains a protein, a
zinc, and a single water if you have multiple temperature coupling
groups. Also I am not sure if settle is going to work properly.
There is no warranty associated with this next portion, I have never
tried it. I have included this just to be explicit about what I am
suggesting. Lets say you use tip4p and oplsaa:
under [ atoms ] add:
2901 opls_113 1 SOL OW 1 0.0
2902 opls_114 1 SOL HW1 1 0.52
2903 opls_114 1 SOL HW2 1 0.52
2904 opls_115 1 SOL MW 1 -1.04
under [ bonds ] add:
#ifdef FLEXIBLE
; i j funct length force.c.
2901 2902 2901 0.09572 502416.0 0.09572 502416.0
2901 2903 2901 0.09572 502416.0 0.09572 502416.0
#endif
under [ angles ] add:
#ifdef FLEXIBLE
; i j k funct angle force.c.
2902 2901 2903 1 104.52 628.02 104.52 628.02
#else
[ settles ]
; OW funct doh dhh
2901 1 0.09572 0.15139
#endif
Then also add:
[ exclusions ]
2901 2902 2903 2904
2902 2901 2903 2904
2903 2901 2902 2904
2904 2901 2902 2903
[ dummies3 ]
; Dummy from funct a b
2904 2901 2902 2903 1 0.128012065
0.128012065
Then go back and add any bonds that you want between this water and
the protein or zinc.
It is unclear to me if the [ exclusions ] section is necessary or even
advisable.
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