On Wed, 16 Jan 2008 22:29:31 +0100 (CET)
"Velia Minicozzi" <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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
-----------------------------------------------------
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