[gmx-users] interchain bond

Velia Minicozzi velia.minicozzi at roma2.infn.it
Wed Jan 16 22:29:31 CET 2008

Hi Xavier,

I think it works I just deleted the 3 H at the N-terminus of the second
chain and when I used merge in pdb2gmx it worked!
Thanks a lot!


On Tue, January 15, 2008 8:50 pm, Xavier Periole said:
> 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
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------

Velia Minicozzi
Department of Physics
University of Rome "Tor Vergata"
Via della Ricerca Scientifica, 1
00133 Rome - Italy
tel. +39 06 72594554
fax. +39 06 2023507


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