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

[Triguero, Luciano O]

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?
 
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