[gmx-users] Adding two peptides in a water box

[Lars.Schaefer at mpi-bpc.mpg.de]

> Hi Everybory,
>
> I would like to simulate the interaction between two separated peptides in
> a water box. Every peptide needs to be N-and C-terminated. I have tried
> different alternatives in order to create the corresponding GROMACS files
> to start my simulation. I have used the GROMACS porograms tools as
> described in the manual. However, I still have some problems and need of
> your expeirences.
>
> This is what I do:
>
> 1.- I start from a pdb of one peptide.
> 2.- Create the gro and top files. In this step I terminate the peptide
> without any problem.
> 3.- Apply corresponding translations and rotation to the existing gro file
> (obtained in step 1) and create a new .gro  file. This one is termed the
> second peptide.
> 4.- Cat them with an editor and save the result in a file named dimer.gro.
> I can visualize it without any problem. So far, everything is going good.
> 5.- HERE STARTS THE PROBLEM. I use dimer.gro as input to pdb2gmx to create
> the new, dimer.top file. The pdb2gmx removes the hydrogens of the N-term
> of one petide and the oxigen of the C-term in the second peptide.
> Although, they are far apart.
>
> Does anyone know how to overcome this porblem?

Hi,
why do you run pdb2gmx for the dimer? run it for the monomer, and then
just put a "Protein 2" instead of a "Protein 1" (or however you name it)
at the end of your topol.top file (just as is done for the water
molecules, ions, etc).
Lars
>

> Thank in advance for you time.
>
> Ciao,
>
> Luciano
>
> Dr. Luciano Triguero College of Art and Science Department of Physics and
> Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box
> 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office:
> 305-284-3938
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