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

[V.V.Chaban]

I believe you need to attach waters to the protein harmonically and
T-couple them separately during MD.




On Mon, Jun 15, 2015 at 3:49 AM, Albert <mailmd2011 at gmail.com> wrote:
> 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
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