[gmx-users] interchain bond

[Velia Minicozzi]

On Wed, January 16, 2008 10:40 pm, Xavier Periole said:
> 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.
>

Yes I have done all this and added a bond in the bond section.

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

I will check tomorrow!

Thank you very much! I didn't find many hints on the manual! The user
group is really useful!
>
>
>
>> 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
> -----------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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>


*********************************
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/
*********************************