[gmx-users] interchain bond

Xavier Periole X.Periole at rug.nl
Tue Jan 15 20:50:03 CET 2008

On Tue, 15 Jan 2008 16:32:54 +0100
  Velia Minicozzi <velia.minicozzi at roma2.infn.it> wrote:
> Dear gromacs users,
> I have two identical peptides which should bind one metal ion. I guess
> I have not understood how I can make this bond.
> I labeled the two peptides with different chain identifier otherwise
> pdb2gmx does not understand that they are two peptides and not one
> protein. The metal is labeled with a third identifier, and I modified
> the ffoplsaabon.itp file inserting this bond and the specbond.dat file.
> Having 3 chains I have 3 different itp files and one top file in which
> all of the itp are called. Unfortunately in none of the itp files nor in
> the top file there is any reference to this bond I created, and after
> some time of MD simulation two of the atoms "bound" to the metal fly
> away even if I use constraints on all bonds.

You have to use the merge option of pdb2gmx, it will generate one topology
of the two peptides and the metal. Then you can add the bond within this
topology file. The numbering of the atoms is important.
If you create a chemical bond between two topologies (peptide-metal) this
will not work.

> I guess I didn't create those bonds correctly. How should I do?
> Any help is welcome!
> Best,
> Velia
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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