[gmx-users] interchain bond

Velia Minicozzi velia.minicozzi at roma2.infn.it
Wed Jan 16 14:26:21 CET 2008

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,


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
>> _______________________________________________
>> 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.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> -----------------------------------------------------
> XAvier Periole - PhD
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------

More information about the gromacs.org_gmx-users mailing list