[gmx-users] how can we merge SOL into protein.itp?

[Albert]

Hello:

I've got two highly conserved crystal water molecules in my simulation 
system, and I would like to treat them as a part of protein. So I am 
must wondering how can we merge it into protein.itp?

I put them into protein.pdb and run command:

pdb2gmx -f protein.pdb -o gmx.gro

and I found that two crystal water molecules was separated from 
protein.itp, and they only explicitly documented in topol.top file.

So I am just wondering how can we solve this problem?

thx a lot

ALBERT