[gmx-users] water in protein itp file
Mark.Abraham at anu.edu.au
Tue Nov 14 04:49:27 CET 2006
> 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
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
4. Sacrifice a goat at the full moon.
Oh, and read Chapter 5 of the manual *really* thoroughly.
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