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

[Mark Abraham]

On Mon, Jun 15, 2015 at 8:50 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.


What are you trying to achieve? Whether you need to do something like you
tried below depends on the objective.

Mark


> 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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