[gmx-users] interchain bond

[Velia Minicozzi]

Thank you Xavier,

but I still have problems because when I use merge, pdb2gmx doesn't want 
that the second peptide has NH3+ and COO- as terminals and doesn't 
understand if I use -ter when I am using -merge, so doesn't create the 
top file.

What do you exactly mean for "the numbering of atoms is important"? I 
tried in two ways:
1. Each peptide starts form one
2. The second peptide numbering starts from the end of the first

in both cases I have the same results and none of them works.

Cheers and thank you,

Velia

Xavier Periole ha scritto:
> 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
> -----------------------------------------------------