[gmx-users] water in protein itp file

[Mark Abraham]

raja wrote:
> Dear gmxions,
> I want to include one crystal water within protein itp, to further
> restrict it by harmonic bond with metal ion at the active site. 
> In other words, one of the water molecules to be treated just likes
> another protein residue by pdb2gmx. How to do that?

Nobody here owes you an answer. This is a fiddly thing to do, and you 
will need to work the details out yourself. I can well understand nobody 
really wanting to get involved. I expect you'd need to

1. Add that water to the .gro file by hand after using pdb2gmx, using a 
residue name distinct from any name other waters might use.
2. Extend the protein+metal [ molecule ] section of your .top by hand to 
add that water, using the information in spc.itp as a model for the 
stuff you're going to need to make water fit. Also add the harmonic bond 
in here.
3. Then use editconf and/or genbox to generate the rest of the solvent, 
and massage the [ molecules ] section of your .top to have the 
appropriate stuff.
4. Sacrifice a goat at the full moon.

Oh, and read Chapter 5 of the manual *really* thoroughly.

Mark