[gmx-users] distance restraints: -merge

[Berk Hess]

>From: "Owen, Michael" <MichaelOwen at creighton.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] distance restraints: -merge
>Date: Tue, 26 Sep 2006 11:10:15 -0500
>
>
>Fellow gmx-users,
>
>I would like to constrain the distance of an ion to specific atoms of a 
>protein.  I recently read a message in which the use of the option -merge 
>in the pdb2gmx program was suggested.  How can I use this option to form 
>these constraints?

The -merge option is useful for merge two molecules.

I assume that in your case the ion consists of just one atom.
Then it is easier to just add this one atom by hand at the end of atoms
of your protein and add the distance restraint.

Berk.