[gmx-users] interchain bond

[Xavier Periole]

On Wed, 16 Jan 2008 22:29:31 +0100 (CET)
  "Velia Minicozzi" <velia.minicozzi at roma2.infn.it> wrote:
> 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!

Cool.

What I meant with the atom numbers is that now you can open your
gro file and look for the atom numbers to bound and go to the itp
file and add a bond (in the [ bond ]section) using these atom numbers.
Previously grompp would have attributed then to the same molecule.
Now they should be bound.

You can check the tpr file using gmxdump -s topol.tpr



> Velia
> 
> 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
> 
> http://biophys.roma2.infn.it/
> *********************************
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------